Clean Water Act: Section 401 Water Quality Certifications

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.

Passed by Congress in 1972, the federal Clean Water Act grants states and Tribal governments the authority to review and approve, condition, or deny proposed projects, actions, and activities directly affecting waters of the United States. In Washington, Ecology is the certifying authority and is responsible for issuance of Section 401 water quality certifications. Tribal governments and the EPA also have this authority on Tribal and nonstate lands.

Under Section 401 of the Clean Water Act, federal agencies can't issue a license or permit before we make a determination on a water quality certification request or waive our right to review. Any conditions that the certifying agency sets then become conditions of the federal permit or license.

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Requesting a 401 water quality certification

The 2020 Rule, now back in effect, requires that all project proponents requesting a Section 401 water quality certification must first file a pre-filing meeting request with Ecology at least 30 days before submitting a 401 request.

To request a 401 Water Quality Certification:

Before submitting a Section 401 certification request, please request a pre-filing meeting with Ecology at least 30 days beforehand. We have developed a pre-filing request form to assist applicants.
At least 30 days after submitting a pre-filing meeting request, applicants may then submit their entire Section 401 request, along with a 401 Request Form, to Ecology and the federal permitting agency.
- For most requests, the federal permitting agency is typically the U.S. Army Corps of Engineers. For hydropower dams, the federal permitting agency is the Federal Energy Regulatory Commission. For National Pollutant Discharge Elimination System (NPDES) permits, the federal permitting agency is the EPA.

Applicants must submit their pre-filing meeting requests, Section 401 water quality requests, and any supporting documents to us electronically at ecyrefedpermits@ecy.wa.gov.

If you are having any difficulties accessing or using these forms, please contact our Federal Permits Unit at ecyrefedpermits@ecy.wa.gov or 360-407-6076.

Examples of projects requiring 401 water quality certification

Section 401 water quality certifications allows us to review and condition projects, actions, and activities that can affect water quality in Washington. For example:

When a port seeks permission to dredge a channel or waterway, we outline where dredge spoils can go.
When hydropower projects request a license for an existing dam or for new construction, we assess whether state water quality standards are met and set conditions to make sure state waters are protected.
We review projects with proposed wetland impacts to protect them during site development and to determine when mitigation is necessary.
When shoreline property owners propose new piers and other structures, we work with them to protect water quality and minimize environmental impacts.

When we issue a Section 401 water quality certification, it means we have determined that a project or action, as proposed or as conditioned, will comply with state water quality requirements and protect aquatic resources.

Certification for specific federal permits and licenses

FERC hydropower licenses

We work with the Federal Energy Regulatory Commission (FERC) to re-license existing dams or license new construction for hydropower dams. When an applicant requests a certification for a hydropower license, we work with the utility or project proponent and review the applicable studies, analyses, and plans. If we determine that water quality standards are attainable, a Section 401 water quality certification is issued with appropriate conditions to make sure environmental standards will be met. These conditions become part of the new FERC license.

U.S. Army Corps of Engineers permits

All projects affecting navigable and protected waters in Washington state, as defined by the federal government, are subject to Section 401 water quality certification. These waters include coastal and marine environments, rivers, streams, lakes, and wetlands. This provides a strong opportunity to protect and enhance water quality, aquatic species and habitats, water resources, coastal resources, floodplains, and other environmental elements. This process excludes hydropower and NPDES-related projects.

EPA and Tribal permits

EPA and Tribal governments use National Pollutant Discharge Elimination System (NPDES) permits to ensure water quality and to limit the quantity of wastewater and stormwater discharge into surface waters like rivers, lakes, and streams. We write NPDES permits for all non-federal discharges in the state, except those on federal and Tribal lands.

Nonfederally regulated waters

Washington state defines state waters separate from the federal government. Projects affecting state waters that don't fall under the federal jurisdiction of "waters of the United States" are not subject to federal 401 water quality certification. However, they are still subject to applicable state water quality and environmental protection laws. This may include ponds, wetlands, and ephemeral streams, etc. that don't meet the definition of "waters of the United States."

Recent Section 401 decisions and public notices

All public notices for Section 401 water quality certification and our recent decisions are listed in our reporting databases. Information for notable Section 401 submissions and decisions also are detailed below.

Notable 401 decisions and requests

Ecology denies without prejudice the 401 Water Quality Certification for Goldendale Energy Storage Project

In June 2021, after a thorough review, we have determined that the information submitted is insufficient to approve an application (submitted by Rye Development, on behalf of FFP Project 101, LLC) for Water Quality Certification for the Goldendale Energy Storage Project.

Our decision is technically referred to as a denial without prejudice. This decision does not prevent Rye Development from continuing to pursue the project. The company can submit a new request when sufficient information is available.

We had one year to make a decision this 401 certification application. As part of the application process, we requested additional information specifically about protecting ground and surface water. We did not receive enough information within the one-year timeframe to support issuing the certification.

For more information about the 401 certification, visit the Goldendale Energy Storage Project website.

EPA's temperature TMDL and 401 certification

In August 2021, the EPA reissued a water improvement plan to reduce temperatures in the Columbia and Snake rivers. The plan, called the Columbia and Snake River temperature TMDL, sets reduction targets for each source of temperature pollution — such as dams, businesses, and sources in tributaries.

Although EPA wrote this TMDL, our agency is responsible for implementing the Washington aspects of it. Since the TMDL identifies the temperature impacts of the dams, we use our 401 certifications as tools to work with EPA and the operators of the federal dams to reduce their temperature impact.

Eight permits issued with 401 conditions for temperature

When federal agencies issue water quality permits, the U.S. Clean Water Act gives states the ability to condition those permits, using a 401 certification, to ensure that they meet state standards. In 2021, EPA released eight draft National Pollution Discharge Elimination System (NPDES) water quality permits to authorize the discharges from the Lower Columbia and Snake River Hydroelectric Generating Facilities (federal dams). In May 2020, we issued conditional 401 certifications that required EPA's final permits to address the dam's temperature-pollution impacts and include the temperature allocations from EPA's temperature TMDL.

The Army Corps of Engineers, operator of the federal dams, appealed our conditional 401 certifications to the Pollution Control Hearings Board, and the Board ruled in our favor on Nov. 3, 2021. EPA has issued all four Columbia River permits and all four Snake River permits.

In January 2022, EPA released for public comment two more draft NPDES water quality permits to authorize discharges from the Grand Coulee Dam and Chief Joseph Dam. We submitted the 401 certifications with conditions for Grand Coulee Dam and Chief Joseph Dam on Sept. 30, 2022. EPA has not yet issued the final Grand Coulee Dam or Chief Joseph Dam permits.

Read the 401 certifications

Grand Coulee Dam (pdf)
Chief Joseph Dam (pdf)

We have now submitted 401 certifications for all 10 federal dams in the state.

EPA plan for Washington and Oregon rivers leaves salmon in hot water is an August 2020 blog post on this project.

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Contact information

Section 401 help
ecyrefedpermits@ecy.wa.gov
360-407-6076

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