Salmon net pen water quality individual permits

We received National Pollutant Discharge Elimination System (NPDES) permit applications from Cooke Aquaculture Pacific (Cooke) requesting to modify its existing water quality permits for four Puget Sound net pens. The company wants to raise all-female, sterile rainbow trout, also known as steelhead, which are native to Washington, instead of non-native Atlantic salmon.

In order to change the species they are farming, the company must go through a multi-agency, multi-step permitting process. Our role is to consider how the new species may affect the discharges from the operation and what is required to be in the permit to ensure that water quality is protected. The Washington Department of Fish and Wildlife (WDFW) has approved and issued their Marine Aquaculture Permit allowing Cooke to farm this native salmon in Puget Sound. WDFW regulates ecological impacts of marine aquaculture to prevent disease and deleterious effects to wild fish stocks. The Washington Department of Natural Resources (DNR) provides state aquatic land leases to Cooke.

Cooke submitted applications and support documents requesting to modify their existing water quality permits for four net pens — one near Hope Island in Skagit Bay, and three in Rich Passage in Kistsap County (see maps below). We updated these permits in July 2019 to include increased protections for water quality based on the lessons learned from the 2017 net pen collapse.

The company wants to raise all-female, sterile rainbow trout, also known as steelhead. As 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, if we modify the permits it will 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.

Modification applications and support documents

Comment period: April 14 - June 8, 2020

This is the first step in Ecology’s process. Following this application comment period, we will review the public feedback and determine if and how to modify the permits. If we decide to modify the existing permits, we will make the draft permits available for public review and feedback; the soonest this may happen is Summer 2020.

We invite you to comment on whether the applications and supporting documents contain all the necessary information needed to permit this species change.

Submitting written comments

The deadline for submitting written comments is June 8, 2020. You can submit comments:

  • Online via the e-Comment form
  • By mail:
    Laurie Niewolny, Water Quality Program
    Washington State Department of Ecology
    PO Box 47600, Olympia, WA 98504

Updated permits issued in July 2019 incorporate lessons learned from the net pen failure

Lessons learned from the net pen collapse at a Cooke Cypress Island site in August 2017 and the investigation are reflected in the updated permits issued in July 2019. To protect Washington waters as much as possible, additional protective measures in the permits include:

  • Increasing underwater video monitoring of net pens
  • Conducting inspections to assess structural integrity of the net pens and submit inspection reports certified by a qualified marine engineer to Ecology
  • Improving net cleaning and maintenance procedures to prevent biofouling and fish escape
  • Requiring the permittee to develop site specific response plans in the event of a fish release, and to conduct and participate in preparedness trainings
  • Requiring improved maintenance of the net pens
  • Maintaining contact information to notify area tribes in the event of a fish release

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.


  • April 2017: Cooke submits applications to renew their permits for all eight of their net pen facilities.
  • August 2017: A net pen owned by Cooke Aquaculture near Cypress Island in Skagit County failed and released Atlantic salmon into the surrounding waters. 
  • March 2018: Governor Inslee signs House Bill 2957 into law. It phases out Atlantic salmon marine net pens.
  • July 2019: Ecology issues permits to four net pen facilities
  • January 2020: WDFW approves change of species to Steelhead with conditions for the protection of native fish and wildlife.
  • February 2020: Ecology receives Cooke's applications for permit modificaiton to raise steelhead. 
  • August 2024: NPDES permits expire

Current permit documents

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.