Skip to content

American Fisheries Society Family of Websites:

Fisheries.org

American Fisheries Society
Family of Websites

Journals

Read our five journals and Fisheries magazine

Gray Literature Database

Find thousands of unpublished agency reports and other information

Annual Meeting

Join us in Columbus in 2026

Divisions, Chapters, Sections

Find an AFS Unit near you or in your area of specialty

Fishbook

Fisheries Collaboration Network

Climate Change and Fisheries

Learn how to communicate the effects of climate change on fisheries

Hutton Junior Fisheries Biology Program

Summer internships for high school students

Community Growth and Connections

Explore our initiatives to build community in the Society and in the fisheries profession

Center for Fisheries Technology and Collaboration

Find fisheries science products and services

Center for Technology and Collaboration

Quick answers to common questions

Other Resources
  • Standard Methods for Sampling North American Freshwater Fish Website

  • Rotenone Stewardship Program Information Site

  • Fishionary: A blog about fish words! 
Latest News
2026 Officer Election Voting Now Open AFS Calls for Continued Protection of Boundary Waters from Mining Proposed Rule Would Undermine Science-based Endangered Species Act Future of Public Trust Resources – Statement of the American Fisheries Society Latest Newsletter
Donate
Login
Logout
$0.00 0 Cart
  • Who We Are

    Who We Are

    Governance

    Learn how AFS is structured

    Divisions, Sections, Chapters

    Find a community in your local
    area or in your expertise

    Committees

    Get engaged and volunteer

    Awards & Recognition

    Nominate your heroes

    Community Growth and Connections

    Learn more about our community-building efforts

    AFS Celebrates 150+ Years

    Explore our history

    AFS Fisheries Partnerships

    Meet our global partners

    Meet the Staff

    Dedicated to serving our members

    Contact Us

    Quick answers to common questions

    Support AFS

    Discover how you can support critical AFS programs

    What Are Fisheries?

    Explore fisheries professions

  • MEMBERSHIP

    Membership

    Learn about membership benefits and member types

    Member Directory

    Find your colleagues

    Types of Membership

    For all stages of your career

    Give the Gift
    of Membership

    Invest in an aspiring fisheries
    professional’s future

    Who Are Our Members

    From students to 50-year Golden Members

    Governance

    Learn about our organization and leadership

    My Account

    Log in to access member benefits or renew

    Join/Renew

    It’s Quick and Easy

    Organizational Membership

    Become a Strategic Partner!

  • POLICY

    POLICY

    Recovering America’s
    Wildlife Act

    Critical funding for state conservation programs

    Climate Change

    Communicate the impacts
    of climate change on fisheries

    Magnuson-Stevens Act

    Ensuring sustainability of marine fisheries

    Waters of the US

    News about Clean Water Act
    jurisdiction

    Water Quality

    Healthy fisheries require healthy waters

    Pebble Mine

    Protecting Bristol Bay salmon fisheries

    National Fish
    Habitat Partnership

    Addressing fish habitat regionally

    Infrastructure

    Funding impacts on fish habitat

    Aquaculture

    Providing food security for the future

    Future of the Nation’s
    Aquatic Resources

    Priorities for US fisheries policies

    Recent Policy Statements

    Official policy statements of AFS

    Policy Letters

    Comments on policy,
    legislation, and regulations

    Sport Fish Restoration Act

    Understanding its importance in funding state agency fisheries management

    Advocacy Guidelines

    For Units and members

    Science Guidelines

    Practicing science appropriately

    Briefings

    Congressional briefings with our partners

    Resolutions

    Member-approved resolutions
    on policy

  • NEWS

    News

    Announcements

    Official AFS news

    Annual Meeting

    News from the meeting

    Members in the News

    Awards and interviews

    Policy News

    Round-up of all policy news

    Beneath the Surface Podcast

    A deep dive into the programs and people at AFS

    Federal Workforce and Budget Cuts

    Resources and Ways to Take Action

    Newsletter

    Bi-weekly newsletter for members and partners

    Press Releases

    News media releases

  • EVENTS

    Events

    Annual Meeting

    Columbus 2026

    Future Annual Meetings

    Where we are heading

    Past Annual Meetings

    Where we’ve been

    World Fisheries Congress 2024

    Seattle, Washington

    Other Past Events

    Past special events

    Fisheries Events Calendar

    Events around the world

    Add Your Event Listing

    Submit your calendar item

  • JOBS

    Jobs

    Career Help from AFS

    Compilation of job listing boards

    Other Career Tips

    Career info for members

    Find a Job

    Listings from all over North America

    Post a Job

    Submit your job opening

  • PUBLICATIONS

    Publications

    AFS Journals Program

    More than 150 years of excellence

    AFS Books Program

    Publish with AFS

    Submit Journal Article

    Reach the right audience for your research

    Fisheries Magazine

    Monthly membership magazine

    Writing Tools

    Guides for authors and other resources

    Fishy Fridays

    Weekly blog highlighting AFS fisheries journal articles

    Bookstore

    Shop more than 180 titles

    Journal Online Access

    Log in to access journal articles

    Gray Literature Database

    Thousands of unpublished agency reports and research

  • Professional Development

    Professional Development

    Continuing Education

    Gain skills and enhance your career

    Professional Certification

    Official recognition of your expertise

    Hutton Junior Fisheries
    Biology Program

    Summer high school
    internship program

    Leadership Opportunities

    Hone your leadership skills, volunteer today!

    Training Opportunities Calendar

    Webinars, online courses, on-site workshops, and field training

    Webinars

    Check out upcoming sessions or browse our library

    More Online Resources

    Practical resources for fisheries professionals

  • Engagement

    Engagement

    Strategic Partners

    See how your organization can partner with AFS

    Support AFS

    Discover how you can support critical AFS programs

    The 1870 Society

    Recognizing generous individual donors who invest in the Society's mission

    2024 Annual Report

    Find out what AFS did for the fisheries community in 2024

    Shop AFS

    Check out the latest AFS merch here

Login
Logout

Hunting, Fishing, and Conservation Groups Oppose Changes to Clean Water Act Section 401 Process

  • October 21, 2019
  • Policy Letters, Water Quality
  • Home
  • Hunting, Fishing, and Conservation Groups Oppose Changes to Clean Water Act Section 401 Process

PDF version

October 21, 2019

Administrator Andrew Wheeler
Environmental Protection Agency
1200 Pennsylvania Avenue NW
Washington, DC 20460

Submitted via regulations.gov

RE: Comments on Docket ID No. EPA-HQ-OW-2019-0405

Dear Administrator Wheeler,

On behalf of our millions of members and supporters, the undersigned hunting, fishing, and conservation groups write in opposition to the Environmental Protection Agency’s (EPA) proposal to make changes to the rules governing states’ and tribes’ Clean Water Act (CWA) Section 401 water quality certification process. We oppose the proposed rule both because it would negatively harm fish and wildlife habitat and because it creates enormous barriers for states and tribes to use 401 certification conditions to protect their important water resources. These barriers shift power that Congress deliberately gave to states away from state agencies to the EPA as well as other federal agencies, some of which have no Clean Water Act authority.

We ask that your agency withdraw this damaging proposal immediately and instead uphold the longstanding cooperative federalism approach that allows states, tribes, and the federal government to work together to protect our shared water resources and the fish, wildlife, and outdoor pursuits that depend on access to healthy wetlands and streams.

The Need for Section 401 of the Clean Water Act
The Clean Water Act is one of our country’s bedrock environmental laws, passed to “restore and maintain the chemical, physical, and biological integrity of the Nation’s waters.” Section 401 is an integral part of the Act. It established an important federal-state partnership, providing states with the opportunity to ensure Clean Water Act protected waterways and wetlands are safeguarded from the adverse effects of activities that need federal permits, such as the construction of dams, diversions, housing and commercial development, roads, bridges, mines, hydropower plants, and pipelines.

While outright denials of certification are rare, states do use their Section 401 authority to condition projects that would harm fish and wildlife habitat. Conditions can allow a project to proceed, albeit with requirements to avoid decreased stream flows, blocked fish passage, increased sedimentation, and/or elevated stream temperatures. For example, in 1986, Washington state stated it would grant a Section 401 permit for a new dam, provided the permittee maintained a minimum in-stream flow below the dam to protect an important fishery along the Dosewallips River near Olympic National Park. The state required these conditions because the impacted waterway was an important spawning and rearing habitat for coho and chinook salmon as well as cutthroat trout. The permittee challenged the state’s decision to require the minimum instream flows; however, in a 1994 7-2 decision, the U.S. Supreme Court held that states could impose conditions based not only on Clean Water Act water quality standards, but also, as the statute said, on “any other appropriate requirement of State law.” (PUD No. 1 of Jefferson County v. Washington Department of Ecology)

Additionally, the recent steps the EPA and the U.S. Army Corps of Engineers have taken – to repeal and replace the 2015 Clean Water Rule with a rule that has a much narrower scope – make maintaining Section 401 state authority even more important. Under the EPA and Army Corps’ new proposed definition of “waters of the United States” (WOTUS), roughly 50 percent of wetlands and 18 percent of the country’s stream miles would lose Clean Water Act protections. The Administration’s proposed WOTUS rewrite would threaten waters that provide habitat for more than half of North American migratory waterfowl, serve as critical spawning grounds for salmon and trout, and provide drinking water for millions of Americans. If the agencies finalize their replacement rule, the EPA’s proposed changes to Section 401 will dramatically undermine the ability of states to protect their streams and wetlands that the Clean Water Act would no longer cover.

In its proposed redefinition of WOTUS, the EPA and the Corps of Engineers repeatedly cite Section 101(b), which highlights Congress’ intention that states have a primary responsibility to “prevent, reduce, and eliminate pollution, to plan the development and use (including restoration, preservation, and enhancement) of land and water resources.” Actions taken by the EPA to limit states’ ability to protect their waterways using Section 401 of the Clean Water Act does not support Congress’ approach to cooperative federalism or its recognition that states will often have a better understanding of how to protect their waterways. We question why EPA does not cite Section 101(b) even once in this new proposal to severely limit state 401 certification authority.

Proposed Rule Takes Away States’ Power to Protect Important Waters by Limiting Time Frame for Review
The proposed rule significantly harms states’ ability to protect their critical waterways by limiting the amount of time states have to review permit applications. The proposed rule would limit the “reasonable time” for state certification to a hard stop one-year maximum, even when an applicant has not provided the state with the information it needs to assess the activity. The proposal would treat a state’s failure to act within one year as a waiver of certification. This may mean that states are forced to provide permits for a project not only without technical information about how the proposed activity would affect a fishery, but also before other critical reviews, such as NEPA, have been completed. Furthermore, the EPA proposes a 30-day limit following when an application is submitted for the state certifying agency to request additional information from the applicant. These limitations could not only force a state to rush certification, or deny the certification entirely, but also encourage applicants not to cooperate with states that request additional information.

These proposed changes could significantly harm fish and wildlife habitat. While states certify most projects in less than a year, in order to do a responsible job, states may need more time to gather information so they can understand the full impact of many large-scale construction projects, such as roads, bridges, mines, and pipelines. Additionally, if applicants refuse to provide enough information for the permitting agency to make a decision, under the proposed rule, EPA would declare that the state has waived its authority to certify, or deny certification, to a project that could destroy fish and wildlife habitat or harm communities’ water supplies.

Proposed Rule Restricts State and Tribal Rights to Condition Projects to Better Protect Natural and Cultural Resources
The proposed rule also severely narrows the scope of review and restricts the types of protective conditions states and tribes can place on federally licensed or permitted activities that threaten state or tribal waters. This greatly undermines state and tribal authority to select conditions that benefit local natural resources, while also allowing the federal activity to move forward. The Clean Water Act explicitly grants states and tribes a broad authority to review federally licensed and permitted projects that will impact local water quality and to certify that these projects comply with state water quality standards and state law.

Currently under Section 401, states can impose conditions on projects to ensure the activity will comply with broader water quality goals and relevant state and tribal laws, including project requirements to allow for fish passage, ensure adequate stream flow, preserve historical resources, and protect habitat. The proposed rule would reject this longstanding interpretation. It would instead replace it with a much narrower reading of the law – one not supported by judicial precedent. It would even allow the federal permitting or licensing agency to reject or ignore state and tribal conditions, based on the federal agency’s interpretation of the appropriate scope of a certification, despite the fact that the Clean Water Act directs that the federal permitting agency shall incorporate state or tribal conditions into the federal permit or license.
The proposed rule would further limit the scope of a water quality certification to only impacts directly from a proposed project’s “point source discharge,” instead of allowing a state or tribe to review the water quality impacts of the project or activity as a whole. The statutory language of the Clean Water Act does not qualify “discharges” as “point source discharges,” and therefore does not limit the term “discharge” only to point source discharges. In fact, it also explicitly allows states to impose conditions based on state authority outside the Clean Water Act. For decades, states have considered broader water quality impacts of activities as a whole when reviewing certifications and this broad interpretation is backed by the courts. In the previously cited 1994 Supreme Court case, the Court established that state authority to make a water quality certification goes beyond the proposed discharge to the broader impacts to water quality of the project.

In addition to redefining “discharge” to focus only on point source discharges, the proposed rule also limits review and conditioning to discharges into “waters of the United States.” As mentioned above, the Administration is currently attempting to reduce the scope of the definition of “waters of the United States,” which would remove more than half our nation’s wetlands and millions of stream miles from federal protection. Limiting the conditions that trigger a Section 401 certification process to waters the current administration considers to be a “water of the United States” would dramatically undermine the ability of states and tribes to protect non-federal waters and could potentially result in not requiring a 401 certification for federally licensed or permitted activities with discharges that impact state or tribal waters that are not considered “waters of the United States.”

Additionally, the EPA proposes to define the term “water quality requirements” that may be protected via Section 401 certifications to mean “applicable provisions of 301, 302, 303, 306, and 307 of the Clean Water Act and EPA-approved state or tribal Clean Water Act regulatory program provisions.” This would prevent states and tribes from using 401 certification to protect their waters under “other state requirements” that do not require EPA approval. These proposed limits on state and tribal certification conditions and denials could result in more projects being denied instead of allowing them to be approved with conditions that are protective of local water quality, cultural resources, and outdoor recreation.

Proposed Rule Improperly Gives the Federal Government the Ability to Override State and Tribal Decisions
As discussed above, Section 401 of the Clean Water Act has been a critical tool to allow states, tribes, and the federal government to cooperatively manage our nation’s shared water resources for nearly 50 years. However, the proposed rule imposes a federal override of certification conditions placed on an approved permit or on a state or tribal denial of a permit. The Clean Water Act does not grant EPA the authority to make autonomous determinations about a state or tribe’s water quality certification. In doing so, the proposed rule would undermine the longstanding system of cooperative federalism in which states and tribes – in partnership with federal agencies – are granted meaningful authority to ensure federally licensed or permitted activities move forward in a way that least harms a state or tribe’s natural resources because this is the one opportunity for states and tribes to weigh in on a project that can impact local waters.

Additionally, during pre-proposal comments, states and tribes expressed to EPA a lack of staff and funding to run existing 401 programs. The Administration’s attempts to reduce federal funding provided to states to implement Clean Water Act programs combined with the proposed rule’s time constraints will only further limit a cooperative federalism approach to protecting the health of the waters we depend on to pursue our outdoor passions.

Conclusion
History shows that Clean Water Act Section 401 works and is a critical tool for states and tribes to protect state and tribal resources from damaging federal projects that will impact water resources within their borders. The proposed rule will dramatically limit longstanding state and tribal authority to ensure that projects move forward with protective conditions to limit damage to fisheries, water quality, wetlands, and access to cultural and recreational resources. States and tribes must have adequate time to review and process complex applications and the ability to impose conditions on permits that will protect water quality, especially given the differences in types of resources and water quality standards between states. Likewise, the federal government should not effectively ignore state decisions it doesn’t like.
Again, we urge you to withdraw this damaging proposal immediately and instead uphold the longstanding cooperative federalism approach that allows states, tribes, and the federal government to work together to protect our shared water resources and the fish, wildlife, and outdoor pursuits that depend on access to healthy wetlands and streams.

Sincerely,

National Organizations
American Fisheries Society
American Fly Fishing Trade Association
Appalachian Trail Conservancy
Backcountry Hunters & Anglers
Fly Fishers International
Izaak Walton League of America
National Wildlife Federation
The Nature Conservancy
Theodore Roosevelt Conservation Partnership
Trout Unlimited

State and Local Organizations
Alaska Backcountry Hunters & Anglers
Arizona Wildlife Federation
Arkansas Wildlife Federation
Association of Northwest Steelheaders
California Backcountry Hunters & Anglers
Colorado Backcountry Hunters & Anglers
Colorado Wildlife Federation
Connecticut Backcountry Hunters & Anglers
Conservation Coalition of Oklahoma
Conservation Council for Hawai’i
Conservation Northwest
Delaware Nature Society
Earth Conservation Corps
Georgia Wildlife Federation
Illinois Backcountry Hunters & Anglers
Iowa Backcountry Hunters & Anglers
Kansas Backcountry Hunters & Anglers
Kansas Wildlife Federation
Louisiana Wildlife Federation
Missouri Backcountry Hunters & Anglers
Montana Backcountry Hunters & Anglers
Montana Wildlife Federation
National Aquarium
Natural Resources Council of Maine
Nebraska Wildlife Federation
Nevada Wildlife Federation
New Jersey Backcountry Hunters & Anglers
North Carolina Wildlife Federation
North Dakota Backcountry Hunters & Anglers
North Dakota Wildlife Federation
Oklahoma Backcountry Hunters & Anglers
Oregon Backcountry Hunters & Anglers
Pennsylvania Backcountry Hunters & Anglers
Planning and Conservation League
South Dakota Wildlife Federation
Tennessee Wildlife Federation
University of Minnesota-Twin Cities Collegiate Club, Backcountry Hunters & Anglers
University of Nevada Reno Collegiate Club, Backcountry Hunters & Anglers
University of Montana Collegiate Club, Backcountry Hunters & Anglers
Virginia Conservation Network
Washington State University Collegiate Club, Backcountry Hunters & Anglers
West Virginia Rivers Coalition
Wyoming Backcountry Hunters & Anglers
Wyoming Wildlife Federation

  • Recent News

    • Is Bigger Better for Hatchery Chinook Salmon? May 1, 2026
    • Webinar: A Perpetual Franchise to Cultivate Oysters April 30, 2026
    • Webinar: Skin Cancer Risk and Outdoor Workers: Early Detection and Sun Protection Could Save Your Life April 30, 2026
    • AFS Calls for Robust Funding for NOAA Fisheries April 27, 2026
    • AFS Urges Full Funding for US Fish and Wildlife Service, US Geological Survey, and US Forest Service April 24, 2026
  • About

    The American Fisheries Society is 501c Non-Profit Society

     

    Donate Now

    Quick Links

    • ABOUT
    • POLICY
    • EVENTS
    • PUBLICATIONS
    • MEMBERSHIP
    • NEWS
    • JOBS
    • Contact Us
    • ABOUT
    • POLICY
    • EVENTS
    • PUBLICATIONS
    • MEMBERSHIP
    • NEWS
    • JOBS
    • Contact Us

    Contact

    • 25 Century Boulevard
      Suite 505
      Nashville, TN 37214
    • (301) 897-8616
    Facebook-f Twitter Instagram Linkedin-in Vimeo-v

    Copyright © 2026 American Fisheries Society | Privacy Policy 

    This website uses cookies to improve your experience. Accept Read More
    Privacy & Cookies Policy

    Privacy Overview

    This website uses cookies to improve your experience while you navigate through the website. Out of these, the cookies that are categorized as necessary are stored on your browser as they are essential for the working of basic functionalities of the website. We also use third-party cookies that help us analyze and understand how you use this website. These cookies will be stored in your browser only with your consent. You also have the option to opt-out of these cookies. But opting out of some of these cookies may affect your browsing experience.
    Necessary
    Always Enabled
    Necessary cookies are absolutely essential for the website to function properly. This category only includes cookies that ensures basic functionalities and security features of the website. These cookies do not store any personal information.
    Non-necessary
    Any cookies that may not be particularly necessary for the website to function and is used specifically to collect user personal data via analytics, ads, other embedded contents are termed as non-necessary cookies. It is mandatory to procure user consent prior to running these cookies on your website.
    SAVE & ACCEPT