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Section 401 Removal/Fill Certification - Frequently Asked Questions

  1. Why do I need a 401 Water Quality Certification from DEQ when I already have a state permit from Oregon Department of State Lands' Removal/Fill program?
  2. Does DSL or US Army Corps of Engineers provide my application materials to DEQ to obtain a 401 WQC for my Removal/Fill project?
  3. Where do I send application materials and water quality related information to obtain a 401 WQC?
  4. When should I apply for a 401 WQC?
  5. How long does the 401 WQC process take?
  6. How does the public participation process work?
  7. How does DEQ conduct a 401 WQC evaluation?
  8. What authority and criteria does DEQ rely on to evaluate projects for 401 WQC?
  9. Who determines if there is a "discharge to waters of the US"?
  10. Is there a fee for 401 WQC evaluation?
  11. Can a 401 WQC be waived and what does this mean for an applicant?
  12. What are common holdups in the 401 WQC process?

Q1:  Why do I need a 401 WQC from DEQ when I already have a state permit from DSLs Removal/Fill program?

A:  Section 401 of the Clean Water Act requires any applicant for a federal license or permit to conduct any activity which may result in any discharge into the navigable waters to obtain a 401 WQC from the state prior to the federal license or permit being issued. This means that, even though you may have obtained a DSL permit, a USACE permit may also be required and this federal permit cannot be issued without a 401 WQC decision by DEQ.

In Oregon, USACE and DSL offer a Joint Permit Application, submitted to both agencies, so that processing can happen concurrently.  In addition, DEQ and USACE offer a single public notice process for the USACE permit and the DEQ 401 WQC. Applying and communicating with USACE, DEQ and DSL at the same time will allow better coordination among all involved agencies and result in a smoother permit process. 


Q2:  Does DSL or USACE provide my application materials to DEQ to obtain a 401 WQC for my Removal/Fill project.

A:  No. The applicant is responsible for providing all pertinent application materials to DEQ, including identifying wetlands and waterways that are impacted and describing what those impacts are and what measures will be taken to protect water quality and beneficial uses.

Although DSL posts most application materials on their website, DEQs process is triggered by the federal (USACE) process. DEQ's review begins, in most cases, when USACE publishes a public notice. The timing of the DSL and USACE public notices and reviews are not always synched up and complete water quality information is not required on the Joint Permit Application submitted to DSL and USACE. 


Q3:  Where do I send application materials and water quality related information to obtain a 401 WQC?

A:  DEQ operates the statewide 401 WQC Program out of the DEQ Northwest Region office in Portland, Oregon. The address is:

401 WQC Coordinator
700 NE Multnomah St., Suite 600
Portland, OR 97232

You can also submit materials and information via email or fax a limited number of pages to 503-229-6957. 


Q4:  When should I apply for a 401 WQC?

A:  As soon as you submit a Joint Permit Application to USACE and DSL. USACE will determine if an existing 401 WQC will cover your project under a pre-certified Nationwide Permit or Regional General Permit. If USACE determines that your project needs an Individual Permit or fits in a Nationwide category that has not been pre-certified, you will have to submit all application materials and water quality information directly to DEQ to begin the evaluation.

For Individual Permit 401 WQCs, DEQ begins the evaluation when USACE publishes a Public Notice to solicit comments on your project. DEQ will request additional information if you have not provided adequate basic application, water quality, project specific, and mitigation information to DEQ. Please include the USACE permit number and applicant contact information with all submissions to DEQ.

USACE cannot issue a permit until 401 WQC has been issued or become waived.


Q5:  How long does the 401 WQC process take?

A:  The Clean Water Act and Oregon Administrative Rules require that DEQ complete a certification decision within a reasonable period of time, (which shall not exceed one year).  However, actual durations of review vary based on the complexity of the project, the quality of the information provided, significance of water quality concerns raised during the public process, and the responsiveness of the applicant. DEQ coordinates with USACE and multiple other agencies (National Marine Fisheries Service, US Fish and Wildlife Service, US Environmental Protection Agency, Federal Highways Administration, US Forest Service, Oregon Department of Fish and Wildlife, DSL, Oregon Department of Geology and Mineral Industries, Oregon Water Resources Department, Oregon Department of Agriculture, Oregon Department of Forestry, etc.). DEQ typically delivers a 401 WQC decision concurrent with the USACE permit decision. This can be as short as 45 days, 2-6 months, or 7-12 months.

Sometimes the permitting process is extended beyond one year. This can happen, for example, when critical information is not available within a year, when the project is modified, or when previously unknown complexities arise. DEQ coordinates with USACE on applications held in abeyance or withdrawn and may request that the applicant withdraw and resubmit a request for 401 WQC.


Q6: How does the public participation process work?

A: 1.

For Individual Permits, USACE issues a 30-day Public Notice and includes DEQs 401 WQC public notice. The intent is to have a single process to solicit comments from the public on the potential impacts of the proposed action under the USACEs authority, as well as impacts to water quality under DEQs authority. The process is described in OAR 340-048-0032. A public hearing may be requested and will be granted at DEQs discretion.  

  2. For projects which fit under a Nationwide permit, but in a category which has been denied 401 certification, DEQ must publish a 35-day public notice to solicit comments on the Findings and 401 WQC decision.This process is described in OAR 340-048-0027. A public hearing will be granted if 10 or more persons (or an organization representing 10 or more persons) request a hearing.

For projects which dont require a USACE permit, but do require a 401 (federal actions which result in a discharge), DEQ must publish a 35-day public notice to solicit comments on the Findings and 401 WQC decision. This process is described in OAR 340-048-0027. A public hearing will be granted if 10 or more persons (or an organization representing 10 or more persons) request a hearing.


Q7:  How does DEQ conduct a 401 WQC evaluation?

A: 1.

Identify waterway(s) affected by the proposal.


Identify beneficial uses of affected water(s).

  • Anthropogenic uses (drinking water, livestock watering, hydropower, fishing, recreation, aesthetics, etc.)
  • Aquatic uses (anadromous fish spawning, rearing and migration; resident fish; aquatic life, etc.)

Identify potential water quality parameters affected by proposal and potential effects to beneficial uses, and conduct an antidegradation review.

Example 1: Sediment is suspended during stream bottom disturbance for dredging.

  • Increased turbidity negatively affects anadromous and resident fish.

Example 2: Pervious ground is converted to pavement, which results in rain picking up deposited pollutants because runoff no longer infiltrates into the ground but now discharges directly to waters.

  • If uncontrolled, toxic pollutants discharged to waterways negatively impact all aquatic life, drinking water, aesthetics, etc.

Example 3: Wetlands between a farm field and a stream are filled.

  • Removal of nutrients (phosphorus and nitrogen) from field runoff by wetland vegetation is no longer possible. This allows nutrients to enter stream in excess of water quality standards and cause algae blooms, which die and decompose depleting oxygen needed by aquatic life.

Identify proposed measures to avoid, minimize, or mitigate water quality impacts.

Example 1: In-water work area isolation measures will be used to minimize turbidity and control distribution.

Example 2: A post-construction stormwater management plan has been developed which provides adequate treatment and control of runoff to remove pollutants before discharging to waters.

Example 3: Compensatory wetland mitigation will be accomplished nearby.


Determine if the proposed measures are adequate, or identify conditions needed to protect water quality standards and comply with regulations.

Example 1: Require work to occur only during the preferred in-water timing window to protect sensitive aquatic species, and only in isolation from flowing waters with application of management measures for rewatering.

Example 2: Require implementation of the approved post-construction stormwater management plan, effectiveness monitoring, and contingency measures.

Example 3: Require interception of field runoff and treatment to remove nutrients prior to discharge.


If conditions cannot be applied to the project as proposed, identify alternatives, methods, or management practices for portions of the proposal to reduce negative effects, protect water quality, and comply with regulations.


If protection of water quality standards, beneficial uses, and antidegradation cannot be assured, the certification must be denied.

Internal coordination among various DEQ programs is frequently required to make informed determinations about potential impacts and avoidance. This coordination occurs between DEQ 401 and various water quality programs (e.g., TMDL Basin Coordinators, Underground Injection Control, Stormwater, Groundwater); Land Quality (e.g., Solid Waste, Cleanup); Compliance and Enforcement; Business Office; Laboratory; and other programs.


The 401 WQC Evaluation and Findings Checklist summarizes the above steps as well as other considerations required by the Clean Water Act and Oregon Revised Statutes and Administrative Rules that must be met before a decision can be issued.


Q8:  What authority and criteria does DEQ rely on to evaluate projects for 401 WQC?

A:  Projects must demonstrate compliance with:


Clean Water Act and related Oregon Administrative Rules

    CWA Section 301
  • Applicable effluent limitations
    CWA Section 302
  • Water quality-related effluent limitations
    CWA Section 303
  • Water quality standards and implementation plans
    OAR 340-041-0001 through 0061 
  • Narrative & numeric criteria and anti-degradation
    OAR 340-041-0101 through 0350   
  • Basin-specific criteria
    OAR 340-042-0025 through 0080
    CWA Section 306
  • National standards of performance for new sources
    CWA Section 307
  • Toxic and pre-treatment effluent standards

Oregon Revised Statutes


ORS 4648B.005 (10)

  • Definition of waters of the state
  • Water Quality Policies
  • Water conservation
  • Protect, maintain, and improve water quality for beneficial uses
  • No discharge without treatment
  • Prevent, abate, or control new and existing pollution
  • Cooperate with other agencies to attain these goals

ORS 468B.020

  • Pollution prevention: 
            Pollution is not a reasonable or natural use of waters
            Prevent new pollution or abate existing pollution
            Use all available and reasonable methods necessary

ORS 468B.025

  • Prohibited activities: 
            Dont pollute waters or place wastes where they could enter waters and dont
             discharge anything that would reduce water quality
            Comply with discharge permits   
            Violations are considered a public nuisance

Oregon Administrative Rules


OAR 340-048-0042

  • Certification decision: 
            Potential alterations to water quality that would cause or contribute to violation of
            Affects to existing and potential beneficial uses of surface and groundwater
            Water quality impacts from activity (use, generation, storage, or disposal of wastes)
            Modifications to water quantity which may affect water quality
            Modifications to groundwater quality which may affect surface water quality
            Water quality impacts from construction of an outfall, intake or other structure
            Water quality impacts from wastewater discharge
            Water quality impacts from construction activities
            Compliance with CWA Section 208 plans (area-wide waste treatment management)   


Q9: Who determines if there is a "discharge to waters of the US"?

The Federal agency considering authorization of the action is responsible for determining if a discharge to waters of the US will result and then advising the applicant to obtain 401 WQC from DEQ. In most cases, this is USACE, who has authority to implement Section 404 of the Clean Water Act and Section 10 of the Rivers and Harbors Act. USACE 404 permits authorized discharge of fill, which is defined in discussions in the Federal Register Volume 67 Number 90, 2002. USACE will also determine whether the subject waterway or wetland is waters of the US. USACE jurisdiction also includes waterways and wetlands which are tributary to or adjacent to waters of the U.S.


Q10:  Is there a fee for 401 WQC evaluation?

A:  Yes, a new fee rule was adopted on July 31, 2013. The current fee schedule is listed in OAR 340-048-0055. Fees are as follows:

Tier Fee
Tier 1 $985
Tier 2A $4,390
Tier 2B $12,105
Tier 3 $17,780
Tier 4 $14,020 per month



Q11:  Can a 401 WQC be waived and what does this mean for an applicant?

A:  Requests for water quality (Section 401) certification of permits issued by the US Army Corps of Engineers for dredged or fill materials under Clean Water Section 404 are processed in conjunction with the federal permitting process and are based on the Corps's public notice.  Typically, these Section 401 certifications are issued within a matter of months, concurrently with Section 404 permit. But certification may be delayed or even denied if an applicant fails to provide additional information as requested by DEQ or fails to provide the information in a timely manner. 

Under Oregon's laws relating to certification under CWA Section 401, DEQ is required to either grant or deny certification. Accordingly, it has not been typical for DEQ to actively waive certification. Under the Clean Water Act, however, the DEQ must act on a request for Section 401 certification within one year or the certification requirement is waived. Typically, DEQ will deny certification if information needed to process the application for certification is not provided or not provided in a timely manner. But on rare occasions, this statutory deadline has been inadvertently missed or other circumstances have resulted in a waiver of certification.

Applicants for certification should note that if certification is waived for any reason, a person involved in fill or removal activities may still liable under Oregon Revised Statutes 468B.025 for causing pollution, placing wastes, (including soils or excavated materials) in a location where they likely to escape or be carried into waters of the state, or violating Oregon's water quality standards as set out in Oregon Administrative Rules, Chapter 340, Division 41. The water quality standard of most concern in this situation is turbidity. That standard typically limits turbidity to an increase of no more than 10 percent above background immediately above the discharge. OAR 340-041-0036. A Section 401 certificate may authorize a short term exceedance of this standard in specified situations involving dredging and construction. In the absence of such a provision in the certificate or if certification is waived, the operation must not exceed the 10% limit.


Q12:  What are common holdups in the 401 WQC process?

A:  The applicant did not submit required Water Quality Specific Information or an approved Land Use Compatibility Statement (LUCS). An application cannot be considered complete without these.

The applicant assumed that USACE or DSL sent DEQ the application materials. Although some application information may be available from DSL or USACE, the applicant is responsible for submitting all pertinent materials to DEQ for consideration during the 401 WQC evaluation. 


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For more information about DEQ's 401 Removal/Fill Certification Program, contact the 401 WQ Certification Coordinator by email.

Oregon Department of Environmental Quality
Headquarters: 700 NE Multnomah Street, Suite 600, Portland, OR 97232
Phone: 503-229-5696 or toll free in Oregon 1-800-452-4011
Oregon Telecommunications Relay Service: 1-800-735-2900  FAX: 503-229-6124

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