Shellfish aquaculture 401 certification

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U.S. Supreme Court stays lower court ruling that vacated 2020 EPA rule

April 6, 2022 - The 2020 EPA Clean Water Act Section 401 Certification Rule was previously invalidated (vacated) by the U.S. District Court for the Northern District of California in October 2021. A group of states and industry groups appealed that decision to the Ninth Circuit Court of Appeals and then sought a stay from the U.S. Supreme Court pending the Ninth Circuit appeal. 

The U.S. Supreme Court granted the stay on April 6, 2022, which reinstated the 2020 EPA Clean Water Act Section 401 Certification Rule until the Ninth Circuit appeal concludes.

We are reviewing our processes to determine what modifications are needed in response to the Supreme Court ruling. Please review our main Section 401 Water Quality Certification page for the most up-to-date information.

In 2020, there were two changes that directly affected shellfish aquaculture in the state of Washington, brought about by two different federal actions:

  • A June 2020 federal court decision affected commercial shellfish growers in the state of Washington by requiring individual aquaculture permits from the U.S. Army Corps of Engineers (Corps)
  • A new EPA rule that modified the permitting process for Section 401 water quality certifications

We have had to modify our Section 401 certification application and review processes to accommodate these federal actions, and coordinate with federal agencies whose processes were affected by the federal lawsuit and EPA rule. This page was created to assist commercial shellfish farmers in completing the required steps to obtain appropriate authorizations to continue operations.

A new normal

Because of requirements mandated by a court ruling that vacated the U.S. Army Corps of Engineers’ (Corps) Nationwide Permit 48 (NWP 48) in Washington state and an a new EPA Section 401 rule, we had to quickly adapt our processes to meet these new requirements and prescribed timelines.

NWP 48 previously authorized most commercial shellfish farms in the state of Washington. Because the NWP 48 general permit is no longer available from the Corps at this time, the Corps must permit all shellfish farms individually in Washington. This individual Corps permit may require Section 401 water quality certification from Ecology, depending on the type of operation and farming activities.

We have heard frustration from the shellfish aquaculture community and their representatives how the court decision and the requirements of the EPA rule are affecting their operations. We are working quickly to address these concerns — including hiring new staff and streamlining our processes to meet this demand.

We appreciate your input and patience as we are still learning how these processes affect the permit coordination and review between us, the Corps, and commercial shellfish farmers. This page outlines the application process as it now stands. To help applicants understand the process, we have prepared in-depth information about what caused all of these changes, along with the following instructions.

Getting started

The Section 401 water quality certification process for shellfish growers. Click the image to enlarge or download a PDF of this graphic.

Under the June 2020 federal court ruling, existing commercial shellfish farms were required to apply for a permit from the Corps before Dec. 11, 2020.

The Corps will review these applications and make a determination to authorize a shellfish operation under:

Either of these permit paths can require an individual Section 401 water quality certification from us.

We are working closely with the Corps to develop a streamlined process to identify whether a commercial shellfish operation will need Section 401 certification. Under this streamlined process, growers must work directly with both the Corps and Ecology. We have created a flowchart to help you visualize this process (see graphic on right).

Under this streamlined process, commercial shellfish operators will contact the Corps to begin their application process.

Pre-filing meeting request

Because a Section 401 certification may be required, commercial shellfish growers should submit a pre-filing meeting request with Ecology as soon as practicable. There is a mandatory 30-day waiting period before a Section 401 certification request can be submitted. This 30-day waiting period is required by the EPA rule and cannot be waived or shortened.

To avoid unnecessary delays, we strongly recommend applicants submit a pre-filing meeting request form around the same time as their initial application with the Corps, even if they anticipate operating under an LOP. That way the 30-day waiting period is started and out of the way.

We will send an acknowledgment that we have received a pre-filing meeting request within 7-10 days after receipt. We will let commercial shellfish farms know when we received their request, identify an agency manager for the project, and when the 30-day waiting period will be met. If you do not receive an acknowledgment email, please contact our team at or call 360-407-6076.

What happens during the waiting period

  • We will review the submitted information and coordinate with the Corps.
  • Our project manager will contact the commercial shellfish farmer to start the conversation about what information and supporting documents may be needed, and the next steps.
  • We will notify shellfish grower and the Corps if a Section 401 water quality certification and Coastal Zone Management (CZM) federal consistency is needed.

Pre-filing meeting

We will hold a pre-filing meeting with applicants on a case-by-case basis to review their project, discuss the type of shellfish aquaculture operation to be certified, and the required supporting documents that need to be submitted for a valid application, if an individual Section 401 water quality certification is needed.

Certain types of operations may not need to continue the Section 401 certification process if we determine the specific operation does not meet the requirements of the EPA rule. If no certification is needed, we will notify the Corps and shellfish grower. If the shellfish grower is notified that an individual Section 401 is required, please submit a valid Section 401 certification application, by following the directions below.

Agency request for comments

As part of the Corps’ LOP process, they will send out an Agency Request for Comments (ARC) to various agencies such as Ecology as well as other federal and state and agencies. The Corps will also coordinate with area tribal governments regarding the permit for a commercial shellfish operation. As part of the ARC process, Ecology will notify the Corps and the shellfish grower whether an individual Section 401 water quality certification and/or CZM federal consistency decision is required.

  • If Ecology determines that no Section 401 water quality certification is needed, the applicant and the Corps can proceed to complete the permitting process for the LOP.
  • If a Section 401 water quality certification is needed, the applicant must follow the instructions below.

Applying for individual Section 401 certification for commercial shellfish aquaculture operations

If a shellfish grower has not already submitted a pre-filing meeting request, follow the instructions above to start the process. A Section 401 certification application can only be submitted after the commercial shellfish grower has submitted their pre-filing meeting request with Ecology and waited a minimum of 30 days. This is a requirement of the EPA rule, and it cannot be shortened or waived.

Starting your application

  1. Complete a Section 401 certification request application form. If you need help completing the form and supporting documentation, please contact us at or call 360-407-6076.
  2. Prepare supporting documents. We will need specific information from shellfish growers to process your request. Growers will work with their Ecology project manager to identify the required documents. If you have a copy of the application materials you previously submitted with the Corps, please submit that information to us. Unfortunately, we do not have access to the Corps’ records. If you do not have a copy of your application package, please contact your project manager to discuss other forms or ways to submit the needed information.
  3. Prepare information regarding water quality monitoring. The EPA rule now requires that a request for a Section 401 contain the methods and means for monitoring the discharges associated with the activities triggering a Section 401. Growers will need to submit information showing how they will be monitoring water quality during farm operations.
  4. Prepare your Coastal Zone Management (CZM) federal consistency form.
    • ​​The Corps will request a CZM form from the commercial shellfish grower as part of the Corps’ permit application. If CZM Federal Consistency is required, the Corps will forward that form to Ecology for a decision.
  5. Other authorizations may be needed, but do not have to be submitted to Ecology with your application, unless requested. This may include:
    • State and local government permits or permissions relevant to your shellfish operation. (e.g., state Department of Health shellfish license, state Department of Natural Resources aquatic lands lease, local government shoreline permits, etc.)

Submitting your application for a Section 401 water quality certification

After the 30-day pre-filing meeting waiting period, applicants can submit their Section 401 certification form and supporting documents to Applicants must also submit the entire application packet to the Corps at the same time.

Application review

After we have received an application, we will evaluate the submitted information and notify the shellfish grower whether we consider their application to be complete and valid.

Complete applications must meet the nine elements defined in the EPA rule. Incomplete applications will not be considered valid. We will notify the grower and the Corps if an application is incomplete and what information or documentation is needed.

If an application is considered to be valid, we will notify both the Corps and the grower. At that time, the Corps can notify us of the reasonable period of time for Ecology to review and issue a decision. A public notice will be issued either by Ecology, or a joint public notice will be issued by the Corps.

Public notice

The public has an opportunity to review and comment on all requests for a individual Section 401 water quality certification and CZM Federal Consistency requests. An Ecology-issued public comment period will be open for 15 to 21 days. A joint public comment period will be will be open for 15 to 30 days.

Approval, denial, or applying conditions to an application

Under Ecology's Section 401 certification authority, we can approve, approve with conditions, or deny an application. If conditions are required for approval, those conditions become part of the permit issued by the Corps.

If an application is denied, the applicant must restart the request process with a new pre-filing meeting request and Section 401 application. If your application was denied, we recommend that you do not start a new application until you have resolved the basis for the denial.


If we do not issue a decision within the reasonable period of time specified by the Corps at the time the application was determined valid, and no official time extension has been granted by the Corps, this constitutes a waiver of Ecology's Section 401 water quality authority and the Corps can issue its permit.


All Section 401 water quality certification decisions can be appealed by the shellfish grower or by any third party to the state Pollution Control Hearings Board. The appeal window is open 30 days from the date of Ecology’s decision.

How we got here

Center for Food Safety v. U.S. Army Corps of Engineers lawsuit

In October 2019, a federal judge in Western Washington District Court issued a ruling stating that the Corps failed to comply with the federal Clean Water Act, the National Environmental Policy Act, and U.S. Endangered Species Act when it reissued Nationwide Permit 48 (NWP 48) in 2017. Before the lawsuit, the majority of commercial shellfish operators in Washington were covered by this general permit, which had been previously reviewed and conditionally approved by Ecology.

In June 2020, the same court vacated NWP 48 in Washington state waters. With no general permit to operate under, the Corps has no choice but to consider each commercial shellfish aquaculture operation and location as a separate permit, which may trigger an individual Section 401 certification and CZM Federal Consistency.

September 2020 EPA Section 401 rule change

The EPA published a formal rule change in the Federal Register on July 13, 2020. This rule became effective on Sept. 11, 2020, changing both the application process and timelines allowed for Section 401 water quality certifications. Before the rule change, we had three different processes for Section 401 certifications, depending on the type of project and federal agency involved. Now, all applications must follow the steps outlined on our Section 401 Water quality certification webpage in order to comply with EPA's latest requirements.

The EPA's process is substantially different from the previous application process. In order for an application to be considered valid and official, EPA’s process must be precisely followed.

Frequently asked questions