Confined Animal Facilities

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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 be receive information about updates or permit development, please contact the following Regional Water Board staff:

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

CAF Program News

Compliance Assistance Workshops to be held during October 2018 (see flyers for more information)

Annual Report Forms are due to the SF Regional Water Board by November 30, 2018. 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

Program Update - June 2015

The Conditional Waiver (R2-2015-0031) requirements apply to all types of dairies located within the boundaries of the San Francisco Bay Region (Region 2), and that are constructed and operating as of June 10, 2015.  To be eligible for waiver coverage, dairies must be able to meet the waiver conditions, including Statewide Minimum Standards (Title 27). 

To apply for coverage, a Notice of Intent (NOI) is due to the Regional Water Board by September 1, 2015. If a dairy has more than 700 adult cows, it is defined by federal regulations as a “large concentrated animal feeding operation”. Such facilities must have a completed Nutrient Management Plan in place, prior to enrolling under the Conditional Waiver.
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:” then press “Go!” The appropriate Regional Water Board information will pop up.

Current Permits, Forms/Factsheets, and Regulations

Permits:

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.

It is important to note that dairies currently enrolled under the Conditional Waiver (Resolution R2-2015-0031) will be required to enroll under Tier II of the General WDRs when the Conditional Waiver expires on June 9, 2020.

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

Conditional Waiver for Dairies:

The Conditional Waiver (R2-2015-0031) requirements apply to all types of dairies located within the boundaries of the San Francisco Bay Region (Region 2), and that are constructed and operating as of June 10, 2015.  To be eligible for waiver coverage, dairies must be able to meet the waiver conditions, including Statewide Minimum Standards (Title 27). 

R2-2015-0031 - Conditional Waiver of Waste Discharge Requirements for Existing Dairies  (complete with attachments)

R2-2015-0031 - Conditional Waiver of Waste Discharge Requirements for Existing Dairies (Adopted Resolution)

Forms/Factsheets:

Dairy Operations

Non-Dairy Operations (equestrian, poultry and others)

Regulations:

Regional and Historical Program Information

Water Quality Concerns for Region 2:
Animal confinement operations such as horse stables, poultry ranches, and dairies, raise or shelter animals in high densities. Wastes from such facilities can contain significant amounts of pathogens, oxygen-depleting organic matter, nitrogen compounds, and other suspended and dissolved solids. In addition, erosion is also a common problem associated with these facilities. Runoff of storm or wash water can carry waste and sediment and degrade receiving surface waters. Ground waters can also be degraded when water containing these wastes percolates into aquifers. The risk of water quality degradation increases during the rainy season when animal waste containment and treatment ponds are often overloaded.

Minimum design and management standards for the protection of water quality from confined animal operations are promulgated in Title 27 (see link above). These regulations prohibit the discharge of facility wash water, animal wastes, and storm water runoff from animal confinement areas into waters of the state. They also specify minimum design and waste management standards including:
  • Collection of all wastewaters;
  • Retention of water within manured areas during a 25-year, 24 hour storm;
  • Use of paving or impermeable soils in manure storage areas; and
  • Application of manures and wastewaters on land at reasonable rates
The Water Board has the authority to enforce these regulations through Waste Discharge Requirements.

Facilities such as the dairies located in Marin and Sonoma counties and horse boarding stables are typical of animal confinement operations within the region.

Regional Cooperative Approach:
Since the 1970s, the cooperative relationship between the Water Board and the dairy industry has been an important aspect of dairy waste control. That relationship has been instrumental in the construction of dairy waste handling, treatment, and disposal facilities in the late 1970s. However, proper waste control management is just as important as the physical facility. Management techniques include routing wash water and drainage to impervious holding and storage areas, constructing manure storage areas controlling both subsurface infiltration and runoff, storm water overflow protection for retention basins, and applying manures and wastewater on land at reasonable rates for maximum plant uptake of nitrogen.

To address dairy waste management concerns, dairy operators in Marin and Sonoma Counties have formed the Animal Resources Management Committee. This committee supports dairy operators and other types of confined animal facilities in their efforts to solve waste control problems and locate technical and financial assistance. The Committee serves as a vehicle through which regulatory agencies can disseminate information on water quality regulations and requirements. This committee does and will continue to play an important role in any successful waste control program.

Additionally, the Southern Sonoma and Marin County Resource Conservation Districts (RCDs) have a cooperative, voluntary program in which a farmer agrees to use the land within its capabilities, develop a conservation plan, and apply conservation practices to meet objectives and technical standards of the RCDs. In turn, the RCD agrees to furnish the farmer with information and technical assistance in order to carry out the conservation plan.

Ag Program and Compliance Assistance Related Links





Since the State Nonpoint Source Policy requires the Regional Water Boards to regulate all nonpoint sources of waste, most of the nine Regional Water Boards have programs in place for confined animal facilities. Links to the other regions' program websites as well as the State Water Resource Control Board and U.S. Environmental Protection Agency websites are provided below:


Helpful Publications and References: