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Manure and nutrient management (CAFO)

Definition

Section titled “Definition”

Manure and nutrient management covers how a dairy collects, stores, treats and applies manure and process wastewater so nutrients (nitrogen, phosphorus) and pathogens do not reach surface water or groundwater.

Who sets the rules:

  • EPA (Clean Water Act): a concentrated animal feeding operation (CAFO) is a point source. A CAFO must not discharge to waters of the US unless the discharge is authorized by an NPDES permit (40 CFR 122.23(d)). After the Fifth Circuit’s 2011 decision in National Pork Producers Council v. EPA, EPA’s 2012 rule removed the duty for CAFOs that only “propose to discharge” to apply; the duty to apply now rests on CAFOs that actually discharge. The effluent guidelines in 40 CFR Part 412 set technical standards for the production area and land application at large CAFOs.
  • States run most NPDES programs and often add their own permits (groundwater, air, state-only CAFO permits), which can apply even when no federal permit is needed.
  • USDA NRCS practice standards (590 Nutrient Management, 313 Waste Storage Facility, and others) are the usual technical basis for plans and cost-share.

A nutrient management plan (NMP) is required for permitted CAFOs. Federally it must address nine minimum elements (40 CFR 122.42(e)(1)): adequate storage of manure and process wastewater, with proper operation and maintenance; mortalities not disposed of in liquid manure, storm water or wastewater systems not designed for them; clean water diverted from the production area; preventing confined animals’ direct contact with waters of the US; chemicals not disposed of in manure or wastewater systems; site-specific conservation practices (such as buffers) to control runoff; protocols for testing manure, wastewater and soil; protocols for land application; and records documenting all of the above. Permittees keep records for 5 years, keep the NMP on site, and file an annual report (40 CFR 122.42(e)(2) and (e)(4)).

How to pull it in DC305

Section titled “How to pull it in DC305”

Mostly not in DC305. Evidence lives in the NPDES or state permit, the NMP, storage inspection logs, manure and soil test reports, land application records (field, date, rate, method, weather), annual reports to the agency, and engineering records for storage structures.

DC305 supplies one input: animal numbers by group (lactating, dry, heifers, calves) for manure-production estimates and for the CAFO size threshold. A head count by group comes from COUNT or SUM by pen or lactation group, e.g.

COUNT BY PEN
SUM BY PEN                head count by pen (SUM with no items counts animals)
ECON\I                    inventory report

Typical range

Section titled “Typical range”

Herd context: US dairies; federal CAFO rules as of 2026. State rules are often stricter.

CAFO size classes for mature dairy cows (milking or dry), confined 45 days or more in 12 months without vegetation in the confinement area:

Class Mature dairy cows Notes
Large CAFO ≥ 700 CAFO by size alone
Medium CAFO 200–699 CAFO if it discharges through a man-made ditch, flushing system or similar device, or directly into waters of the US that originate outside and pass through the facility or contact the animals
Small < 200 CAFO only if designated by the permitting authority

Heifers and other cattle that are not mature dairy cows are counted in their own class: a Large CAFO at 1,000 or more head (300–999 for Medium). Thresholds as of November 2026, 40 CFR 122.23(b).

Large CAFO technical standards (40 CFR Part 412) include:

  • Production area (412.31(a)): no discharge except overflow from storage designed, built, operated and maintained to hold all manure and wastewater plus the runoff and direct precipitation from a 25-year, 24-hour rainfall event.
  • Inspections (412.37(a)): water lines daily; storm-water diversions and manure and wastewater impoundments weekly; a depth marker in open liquid impoundments, with depth recorded weekly.
  • Testing (412.4): manure analyzed for nitrogen and phosphorus at least once a year; soil analyzed for phosphorus at least once every 5 years.
  • Setbacks (412.4): no manure application closer than 100 ft to down-gradient surface waters, open tile line intakes, sinkholes, agricultural well heads or other conduits to surface waters; or a 35-ft vegetated buffer instead; or an alternative shown to give equal or better reductions.
  • Records kept 5 years from creation (412.37(b), (c)); permitted CAFOs file an annual report.

The “AFO” definition behind all of this (40 CFR 122.23(b)(1)): animals confined and fed for a total of 45 days or more in any 12-month period, in an area where crops, vegetation or forage are not sustained in the normal growing season.

Requirements change; confirm the current version with the program or regulator. This page is not legal advice.

Common mistakes

Section titled “Common mistakes”
  • Counting only milking cows for the size threshold; dry cows count as mature dairy cows, and heifers and calves are counted in their own classes.
  • Plan on paper, not in practice: application rates or fields in the records don’t match the NMP.
  • Missing inspection logs for daily and weekly checks.
  • Storage too full going into the wet season, with no freeboard.
  • Applying to frozen, saturated or snow-covered ground, or just before forecast rain.
  • Old manure and soil tests used for application rates.
  • Ignoring setbacks around wells, ditches and tile inlets.
  • Mortalities, milk-house waste or chemicals put into storage without being covered by the plan.
Section titled “Related”