Department of Ecology News Release - December 6, 2022

Ecology updates clean water permit for large livestock operations and manure lagoons

New permit requirements include more groundwater monitoring

The CAFO permit is how Ecology oversees manure management at permitted livestock operations across Washington.



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After reviewing more than 400 comments on a draft permit released earlier this year, the Washington Department of Ecology is issuing an updated final version of the Concentrated Animal Feeding Operation (CAFO) water quality permit. Effective Jan. 6, 2023, the updated permit is how Ecology oversees manure management at permitted livestock operations across Washington.

The permit is designed for large commercial operations, such as operations with more than 200 head of dairy cows, 750 pigs, or 9,000 chickens. Effective manure management at large livestock operations helps keep nitrates, harmful bacteria, excess nutrients and other pollutants out of surface and ground water.

There are currently 24 CAFOs regulated under Ecology’s permit. Ecology regulates these facilities because either they released waste that entered surface or ground water, or they voluntarily chose to come under the permit.

The Washington State Department of Agriculture is the principal inspector of dairies and partners with Ecology to implement this permit.

Permit Revisions

Ecology updates water quality permits every five years. As part of this process, Ecology considers the agency’s experience implementing the permit, including inspections and enforcement actions, updated science, permit appeal decisions, and feedback received during the comment period.

Ecology accepted public feedback on the draft permit from June 22 - Aug. 17, 2022 and held two virtual hearings. Key updates include:

Ground and surface water monitoring

  • Requires groundwater monitoring for all medium and large CAFOs located in areas most vulnerable to nitrate contamination, including the Lower Yakima Valley. The Nitrate Project Story Map shows nitrate priority areas in Washington, with additional information found on the Nitrate in groundwater webpage. This monitoring requirement is in addition to the requirement Ecology proposed.
  • Establishes procedures for when and how groundwater monitoring needs to happen in areas surrounding potential pollutions sources – such as animals, manure storage, and manure application sites- to best protect groundwater from contamination.
  • Clarifies the sampling actions permittees need to take if they have polluted surface water.

Manure pollution prevention

  • Pollution prevention plans are now required when permittees submit their permit application and will have a public comment period.
  • Revises how new manure lagoons must be designed, providing consistency with federal recommendations.
  • Updates how the distance between the lagoon liner and groundwater is measured.
  • Updates requirements for storing solid manure to best protect groundwater.

Managing manure lagoons

  • Clarifies the process to improve an existing manure lagoon to better protect water quality. This includes requiring lagoon assessments be conducted by qualified experts.

Restrictions for applying manure on land

  • Extends restrictions to prohibit applying manure to land that will soon become saturated based on future rain forecast. This will reduce the potential for manure to move off the field and into surface water.
  • Offers a new option to submit alternatives to the standard method for calculating manure application start dates, in response to comments and data received on the growing season for Eastern Washington permittees. Any alternatives to TSUM200 requires public notice and review.
  • Ecology heard from permittees that many crops are harvested after Oct. 1. In response, the previous requirement for collecting soil samples by Oct. 1 now matches University Extension guidance for Post-Harvest Soil Testing. Soil samples must now be collected after crop harvest and before an accumulation of three inches of precipitation and irrigation water.

Ecology had proposed language clarifying the options around stream protection areas but based on feedback received during the comment period, decided to maintain the current permit language.

The updated permit is effective in 30 days, starting on Jan. 6, 2023. To view the permit, response to comments, focus sheet (English and Spanish) and all other related materials, visit

Contact information

Colleen Keltz
Twitter: ecologywa