Regulation 81 (5 CCR 1002-81) & 61 (5 CCR 1002-61):
The current version of Colorado’s Regulation 81 – the state regulation that governs concentrated animal feeding operations (CAFOs) and smaller animal feeding operations (AFOs) – became effective in November, 2013.
Regulation 81 requires that CAFOs adhere to three (3) broad compliance principles: 1) Register the CAFO with the state, 2) Develop and implement a Facility Management Plan (FMP) that protects surface and groundwater, and 3) monitor and keep records. These broad requirements are the same for both permitted and non-permitted 
CAFOs.
Another regulation – Regulation 61 – also governs CAFOs – specifically permitted CAFOs, which are CAFOs that choose to get coverage under the state discharge permit. The discharge permit allows the permit holder to legally discharge wastewater as long as the facility is compliant with its permit at the time the discharge occurs.
Is it wise to obtain CAFO discharge permit coverage? Often the answer is yes. However, the topography of some CAFOs in Colorado is such that a discharge is unlikely. These CAFOs may choose to operate without a discharge permit, but they are still required to register their operation with the Colorado Department of Public Health and Environment (CDPHE) Environmental Ag Program (EAP). CAFO operators that choose to operate without a discharge permit need to be aware that a reported discharge from the facility may result in the issuance by the CDPHE of a Notice of Violation, with corresponding monetary penalty, compliance order, and discharge permitting requirement.
The decision to operate with or without a permit should be carefully weighed, with a clear understanding of local topography and drainage characteristics, as well as pond storage capacity, land application acreage and de-watering infrastructure, field drainage characteristics, and personal risk tolerance. If you are wondering which option if best for your operation, feel free to call me and we can discuss the pros and cons.
The full version of Regulation 81 regulation is available at:
https://www.colorado.gov/pacific/sites/default/files/Regulation-Num-81_AFO-Control-Regs.pdf
Section 61.13 of the regulation deals with permitting of Housed Commercial Swine Feeding Operations (HCSFOs). Section 61.17 covers Concentrated Animal Feeding Operations (CAFOs). The full version of Regulation 61 is available at:
https://www.colorado.gov/pacific/sites/default/files/Regulation-61.pdf