National Pollutant Discharge Elimination System (NPDES)

Concentrated Animal Feeding Operations

California has approximately 2,200 dairies with an average size of about 700 milk cows. There are also several hundred feedlots, poultry operations, and other animal feeding operations (AFOs) in the State. California regulations refer to these operations, including concentrated animal feeding operations (CAFOs), as “confined animal facilities” (CAFs). The exact number of facilities that are CAFOs based on animal populations is unknown but is estimated at between 1,000 and 1,200.

The State Water Resources Control Board (State Water Board) and nine semiautonomous Regional Water Quality Control Boards (Regional Water Boards) protect water quality in California by regulating wastes including manure at CAFs. State regulations that apply to CAFs are in the California Code of Regulations, Title 27, Division 2, Chapter 7, Subchapter 2, Article 1.

Each Regional Water Board develops the regulatory program it uses for CAFs. Most of the commercial CAFs are in the Central Valley Region, including over 80 percent of the dairies. There are about 150 dairies and feedlots in the Santa Ana Region and about 200 dairies (mostly smaller facilities with less than 300 milk cows) in the North Coast and San Francisco Bay Regions. There are also some CAFs in other regions, including a few CAFOs. Dairies and feedlots in the Santa Ana Region operate under a General NPDES permit that requires preparation of an engineered waste management plan. Most of the CAFs in the Santa Ana Region do not apply manure to cropland.

The Central Valley Regional Water Quality Control Board was developing a general NPDES permit for dairies, but stopped when the Second Circuit Court of Appeals ruled that only facilities discharging to a water of the United States need a permit. Such discharges are prohibited at CAFs in California, and as a result of a strong enforcement program, few of these discharges occur. The Central Valley Water Board is now developing a general Waste Discharge Requirements (WDR) Order to regulate the dairies. The WDR Order is essentially a state permit, and a tentative version of the order is expected in mid-2006.

The WDR Order will require the dairies to develop and implement nutrient management plans and to submit annual reports. The permitted facilities will pay an annual fee that is based on animal population and ranges from $200 to $4,000 plus a surcharge to support the Surface Water Ambient Monitoring Program (SWAMP). Since impact to groundwater is the major concern at these CAFs, the WDR Order is expected to require groundwater monitoring at some facilities.

As part of the WDR Order implementation process, in October 2005 dairies in the Central Valley Region were required to submit a Report of Waste Discharge (ROWD) and pay a filing fee equivalent to the first annual fee. Approximately 99% of the 1,650 dairies did so. A major reason for the high compliance rate is that California Dairy Quality Assurance Program (CDQAP) provided training and assistance to the dairy operators. More information on the CDQAP is available on the Internet at:

Air emissions from dairies are a major concern in some areas of California. The San Joaquin Valley Air Pollution Control District has developed draft Best Available Control Technologies (BACT) to address air emissions at dairies - Recommendations to the San Joaquin Valley Air Pollution Control Officer Regarding Best Available Control Technology for Dairies in the San Joaquin Valley.

Questions or Comments

If you have any questions or comments, please contact:

Brianna St. Pierre
Senior Engineering Geologist
(916) 966-3827

Kelsey Moore
Environmental Scientist
(916) 323-0877