Salmon net pen water quality permits

Multiple agencies are involved in making sure fish aquaculture that uses net pens in Puget Sound, meet the required laws, rules, and regulations.

  • We issue individual National Pollutant Discharge Elimination System (NPDES) water quality permits to make sure any release (discharge) of wastewater meets Washington's water quailty standards.
  • Washington Department of Fish and Wildlife (WDFW) regulates ecological impacts of marine aquaculture.
  • Washington Department of Natural Resources (DNR) provides state aquatic land leases.

Cooke Aquaculture permit modifications to raise steelhead

We determined the change of fish species from Atlantic salmon to steelhead is not likely to change the effect on water quality. So we modified the permits for the four facilities to allow Cooke Aquaculture to raise all-female, sterile steelhead (also known as rainbow trout). Because steelhead are native to Washington, they are not part of the 2018 law phasing out non-native species in marine fish farming by 2022. However, the modification does not extend the life of the permits, which expire in 2024. The current permits were originally issued to allow for two years of closure activities and monitoring after the facilities aquatic lands leases from the DNR expire in 2022. The location of the net pens are: one near Hope Island in Skagit Bay, and three in Rich Passage in Kitsap County (see maps below)

In the final modified permits, we included all water quality-related WDFW mitigations and took the opportunity to further strengthen the permit to protect water quality. Changes to the permits include:

  • Clarifying that any fish reared in Cooke’s net pens are prohibited from release
  • Adding requirements and details on how to notify state agencies of events that could potentially lead to fish escape
  • Increasing monitoring and reporting of potential fish escape during stocking and harvesting
  • Adding reporting for fish feed consumption
  • Adding details on how nets must be maintained
  • Adding a requirement to study new technologies and propose alternatives that reduce or prevent discharge of uneaten feed or metabolic waste

Comments on the permits

We held a comment period on draft modifications from Sept. 9 to Oct. 26, 2020, and a public workshop and hearing Oct. 14, 2020, to explain the proposed changes to the permits. There were a total of 147 comment submissions from individuals or organizations via eComments, email, mailed-in letters, and hearing testimony. We compiled all the comments submitted and reviewed each submission.

During this comment period, we received many comments that proposed additional changes to the permit and suggestions that were outside the scope of our permitting authority. Our Responsiveness Summary* contains a summary of comments we received and our responses. 

*Note: Because the only difference between the four individual permits is the location (see permit links below), the permit information and responsiveness summary is the same for each facility. For ease of review, we have linked to the Clam Bay responsiveness summary (Appendix A) in the statement of Basis. However, you can find all of the documents for each location linked from the Facility Summary page below. 

Current permits

Why do net pen operations need a NPDES permit? 

A NPDES permit is the tool that requires best management practices, monitoring, and reporting to ensure water quality standards are met. These facilities are operated to rear fish for harvest and market sale. Uneaten fish food and fish feces are the primary pollutants produced as a result of the operation of these facilities, as well as any accidental release of fish. The requirements in the permit allow us to enforce that facilities are meeting water quality standards.


  • August 2024: NPDES permits expire.
  • Jan. 6, 2021: Ecology issues modified permits for Cooke to raise Steelhead
  • Fall 2020: Ecology holds a public comment period on modified permits
  • Spring 2020: Ecology holds a public comment period on applications to modify permits.
  • Feb. 2020: Cooke applies to Ecology for a permit modification to raise steelhead.
  • Jan. 2020: WDFW approves change of species to Steelhead with conditions for the protection of native fish and wildlife.
  • July 2019: Ecology issues updated permits to four net pen facilities.
  • March 2018: Governor Inslee signs House Bill 2957 into law. It phases out Atlantic salmon marine net pens.
  • April 2017: Cooke submits applications to renew their permits for all eight of their net pen facilities.
  • Aug. 2017: A net pen owned by Cooke Aquaculture near Cypress Island in Skagit County failed and released Atlantic salmon into the surrounding waters. 

Locations of net pens

Three salmon net pens – Clam Bay, Fort Ward, and Orchard Rocks in Rich Passage of Kitsap County. 

Northern most net pen – Hope Island in Skagit Bay of Skagit County.