Confined Animal Facilities

Receive notifications, updates and other correspondence by e-mail. Subscribe on-line to our Confined Animal Facility Program, electronic mailing list.

As of January 2023: Website Updates in Progress. Please email for copies of current annual reporting and enrollment forms.

The San Francisco Bay Regional Water Quality Control Board regulates several types of confined animal facilities (CAFs). CAFs are operations where animals are confined and fed in an area that has a roof or is devoid of vegetation, generating solid and liquid manure wastes that may be collected and disposed of on land. Within the San Francisco Bay Region, the primary types of CAFs are dairies, horse facilities, egg, chicken, and/or turkey production facilities, with the majority of animal waste produced by cow dairies within the counties of Marin and Sonoma. There are approximately 41 dairies currently operating within this Region, with total herd sizes averaging 200-300 head.

This Region's CAF regulatory program includes a Conditional Waiver of Waste Discharge Requirements (Conditional Waiver), for existing dairies (enrolled in 2015) and General Waste Discharge Requirements (General WDRs), for all types of CAFs not currently enrolled under the Conditional Waiver and that are located within certain watersheds. This program requires structural and non-structural management measures for all confined production areas, land application areas and grazing operations, as well as a site-specific monitoring program.

If you operate a CAF (including horse boarding, poultry or other animal types), check the current permits section to see if the General WDRs apply to you.

Staff Contacts

If you have questions about the Confined Animal Facility Program or wish to receive information about updates or permit development, please contact the following mailbox:

Mailing address:
San Francisco Bay Regional Water Quality Control Board
1515 Clay Street, Suite 1400
Oakland, CA 94612

CAF Program News

Annual Report Forms are due to the SF Regional Water Board by November 30th. Dairy and Tier 1 (horses and other animal types) forms can be found here:

Program Update - June 2016

On June 8, 2016, the San Francisco Bay Water Board adopted General Waste Discharge Requirements (Order No. R2-2016-0031) for all types of confined animal facilities within the region. Order No. R2-2016-0031 rescinds and replaces Order No. R2-2003-0093, General Waste Discharge Requirements for Confined Animal Facilities. The updated Order clarifies the regulatory requirements for confined animal facilities (CAFs) that are not currently covered under the Conditional Waiver of WDRs for dairies (2015 Dairy Waiver) adopted by the Board in June 2015, including non-dairy CAFs, e.g., horse-boarding facilities.

The San Francisco Bay Basin Plan specifies implementation measures for each categorical pollutant source identified as contributing to the water quality impairment in specific watersheds. Livestock grazing lands, and confined animal facilities, including dairies and equestrian facilities, are identified as categorical pollutant sources, in certain watersheds, that are required to implement site-specific management measures to control and reduce animal waste and sediment runoff to receiving waters. The updated WDRs will implement the Basin Plan by requiring management measures for all types of CAF pollutant sources in the designated impaired watersheds.

Additionally, the scope of coverage in the revised WDRs extends to former CAFs that, although currently dormant, may re-open at some point in the future. As required by the California Environmental Quality Act of 1970, a proposed Mitigated Negative Declaration has been prepared and will be included with the Tentative Order when it is circulated for public review. Water Board staff anticipate that all documents will be released for public review and comment no later than the end of February 2016.

Response to Public Comments:
The General WDRs were circulated for public review beginning on March 15 and ending on April 29, 2016, and we received six comment letters. Our written response to these comments was provided in the Board hearing agenda package and is also provided here:

Response to Written Comments Received on General Waste Discharge Requirements for Confined Animal Facilities within the San Francisco Bay Region, dated June 8, 2016

Current Permits, Forms/Factsheets, and Regulations


General WDR for all types of CAFs:

The General WDRs apply to commercial confined animal facilities including:

  • Existing operating dairies;
  • Existing confined animal facilities located in water quality impaired watersheds and identified as a categorical pollutant sources in Chapter 7 of the Basin Plan;
  • Other confined animal facilities that the Water Board determines need coverage under the proposed General WDRs;
  • Confined animal facilities that are dormant and inactive as of the adoption date of the General WDRs, but are subsequently reopened as a confined animal facility; and
  • New or expanded confined animal facilities that can demonstrate compliance with the California Environmental Quality Act.

Watersheds with waterbodies currently identified as impaired due to CAF (other than dairy) related pollutants include: Napa River, Tamales Bay, San Pedro Creek and Pacifica State Beach and San Vicente Creek.

To apply for coverage, a Notice of Intent (NOI) for existing facilities is due to the Regional Water Board by October 31, 2016. For newly opened facilities, discharges must submit the appropriate NOI form provided below.

To see if your facility is within Region 2, please visit:

Enter your address in the bottom text box titled “To find the Regional Water Board for a particular location, click on the map or enter a street address.

General WDR Documents