Skip to main content

Manure Management


Modern day agriculture operations are both large and diverse often including both crop and livestock production. The increased size and density of large, confined animal feeding operations (CAFO’s) across America has led to the development and implementation of Government / Environmental regulations to ensure the protection of the countries water, soil, and other natural resources. CAFO operators are required to obtain a state permit from the local Department of Environmental Quality (DEQ) every 5 years and maintain annual compliance documentation in the event of an audit. Adherence to these protocols is important to ensure continued compliance and ultimately your permission to operate. 


If you are thinking of starting a new CAFO operation you will first need to obtain a permit to operate from the DEQ. Once approved, this permit will need to be updated and renewed every 5 years as per the DEQ requirements. At the time of writing a CAFO permit application or renewal consists of 3 things which must be completed and submitted to the DEQ:

  • Notice of Intent (NOI),
  • Nutrient Management Plan (NMP), and
  • CAFO Annual Report (CAFO-AR)

These documents help outline and describe your specific CAFO operation including projected manure volumes and how the manure will be handled or disposed of. This process is also used to identify any areas of concern that may need to be addressed including proximity to surface or groundwater and the location of sensitive wildlife habitats. Once submitted the DEQ will review your application and either approve your permit or request further action to be taken before issuing your general permit.



Once approved for your CAFO permit the DEQ has implemented ongoing compliance measures to minimize offsite pollution and the maintain protection of the states natural resources. Some of the on-going compliance requirements for CAFO operations in Montana include:

  • CAFO Annual Report (CAFO-AR, formerly AR-2),
  • Notification of Discharge (CD),
  • Manure Sample Analysis (Annually),
  • Soil Sample Analysis (Every 3 years),
  • Daily / Weekly / Monthly inspections as outlined by your general permit, and
  • Manure Application Information including transfers and land applications (Annual)

Ensuring the proper collection and reporting of information for your CAFO operation will both ensure continued compliance of your operation and piece of mind if a when your operation is audited. Typically, each producer is audited by the DEQ once every 5 to 7 years and it is imperative to have both your operation and documentation to ensure the audit is a smooth process. From my experience they like to show up during busy times of the year (seeding, harvesting) and not being organized can make the process more stressful than it needs to be.


During the time of your CAFO operation it is likely you will be subject to a compliance audit by the DEQ. DEQ audits are typically comprised of two elements:

  1. Document Review
  2. Site Inspection

During the document review you may be required to produce any of documentation as required by your CAFO permit for the previous 5 year period. Although individual permits may vary, typical items may include:

  • Inspection signoff forms (daily/monthly/yearly)
  • Manure application information (yearly)
  • Soil sample analysis
  • Manure sample analysis
  • CAFO General Permit
  • Annual Reporting forms

During the site inspection you will be required to show the inspector around the facilities including areas such as; lagoons, stacking pits, mortality disposal areas, application equipment storage and the exterior of the barns.


During your CAFO operation if you are deemed to be in breach of compliance with your CAFO’s Nutrient Management Plan you may be subject to one or more punitive actions as set out by local authorities including:

  • Potential loss of FSA or NRCS program payments or cost-sharing support
  • Fines for non-compliance with CAFO requirements
  • Increased costs because of over application of nutrients
  • Loss in yield because of poor nutrient management practices
  • Legal action if laws and/or regulations have been violated