Permit Application Public Notices

The United States Congress authorizes the U.S. Army Corps of Engineers to regulate activities that may impact wetlands and waters of the United States. This authority is granted and defined under Section 10 of the Rivers and Harbors Act of 1899 and Section 404 of the Federal Water Pollution Control Act Amendments of 1972, also known as the Clean Water Act.

Public involvement is a key element of the Corps’ permit review process. During an application review, the Corps considers the views of other federal, state and local agencies, Native American tribes, interest groups, and the general public. The results of this careful public interest review are fair and equitable decisions that allow reasonable use of private property, infrastructure development, and growth of the economy, while offsetting the authorized impacts to the waters of the United States.

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Portland District
Published Aug. 5, 2022
Expiration date: 9/3/2022

Application for Permit

Issue Date: August 4, 2022
Expiration Date: September 3, 2022
U.S. Army Corps of Engineers No: NWP-2019-545/2

30-Day Notice  

Interested parties are hereby notified the U.S. Army Corps of Engineers, Portland District (Corps) has received an application for a Department of the Army permit for certain work in waters of the United States, as described below and shown on the attached drawings. The Corps is soliciting comments on the proposed work.

Applicant:    Oregon State University
                        Attention: Scott Bond
                        850 SW 35th Street 
                        Corvallis, Oregon 97333
                        Telephone: (541) 974-2520

Applicant’s Agent:     Pacific Habitat Services, Inc. 
                                        Attention: John van Staveren
                                        9450 SW Commerce Circle
                                        Suite 180
                                        Wilsonville, Oregon 97070
                                        Telephone: (503) 570-0800

Location: The project site is located in Yaquina Bay at 2030 SE Marine Science Drive in Newport, Lincoln County, Oregon. The site is in Section 17A, Township 11 South, Range 11 West. Latitude and Longitude: 44.625578 North, 124.045051 West

Waterway: Yaquina Bay; The location of the line of mean high water and high tide line shown on the project drawings have not yet been verified by the Corps. If the Corps determines the boundaries of the wetland/waters are substantially inaccurate a new public notice may be published.

Project Purpose: The applicant’s stated purpose is to improve and repair the Oregon State University (OSU) Ship Operations Dock in Yaquina Bay to ensure the dock can berth the longer research vessel Taani with safe operating conditions.

Project Description: OSU proposes to modify their existing ship dock facility to berth the new research vessel (RV) Taani. The project would have both in-water and over-water work components, including groin repairs, bulkhead repairs, and dock reconstruction and expansion.

To repair the existing groin leading to the ship’s operations dock, the applicant would discharge riprap within the existing groin footprint. OSU would remove up to 310 cy and discharge up to 155 cy of riprap within 13,800 square feet below the Mean High Water (MHW). OSU would remove up to 1,530 cy and discharge 325 cy of riprap within 13,800 square feet below the HMT. Old rock would be removed from the groin using an excavator that would grab the rock using a bucket. The excavator would work from the top of the groin. Prior to starting work, two lengths of turbidity curtain would be placed outside of the work area to contain any debris. The work would be conducted at lower tides when the likelihood of creating turbid conditions is less. The old rock would be removed to an upland site. The new riprap would be placed on top of the areas where former riprap was located, though a one-inch-thick layer of filter fabric would be installed prior to discharge of the new riprap. 

To repair the existing bulkhead, a sheet pile bulkhead would be constructed in the dry, replacing the current damaged bulkhead.

To replace the existing dock, OSU would install additional permanent and temporary piling, as well as temporary anchors to secure equipment during in-water work. OSU would also construct new features above the water, including a new 5,347 square foot trestle and dock, new 480 square foot float, and a new 386 square foot catwalk. A total of 866 square feet of the structure would allow light transparency. 

Prior to constructing the new dock, the applicant would remove the existing 1960s dock, including its opaque wooden decking. The removal includes the 4,640 square feet of the existing trestle and dock, 800 square feet of the existing float, 772 square feet of the existing catwalk, and 40 square feet comprised of an existing septic tank. A total of 6,252 square feet of opaque material would be removed.

As part of the existing dock structure removal work, OSU would permanently remove 80 cubic yards (cy) of pilings from below the HMT to remove 70, 12-inch diameter creosote coated plumb wooden piles within 60 square feet of Yaquina Bay. OSU would permanently remove 40 cy of pilings from below the HMT to remove 36, 12-inch diameter creosote coated batter wooden piles within 30 square feet of Yaquina Bay. OSU would remove and replace 1,480 cy of pilings from below the HMT to remove and replace 92, 24-inch diameter steel piles within 290 square feet Yaquina Bay.  

OSU would install 10, 24-inch diameter temporary steel piles for dock installation, which would cover 8 square feet of Yaquina Bay. OSU would also install 4 concrete blocks to temporarily anchor seawater intake pipes that cover 48 square feet of Yaquina Bay. The piling and anchors would be in place no longer than the length of the in-water work period and would be removed at the conclusion of the dock construction work.

The existing creosote piles would be dislodged with a vibratory hammer and slowly lifted from the sediment and placed into a containment basin. The applicant would begin pile installation with a vibratory hammer and then switch to an impact driver for at least 10-20 feet due to depth needs for geotechnical stability.  Piling installation is anticipated to take 30 days with approximately 50-80 minutes of impact hammer use per day.
All heavy equipment would access the project are via floating barge and the overall project mobilization would occur along with implementation of the erosion control measures such as floating booms. Prior to starting work, two lengths of turbidity curtain would be placed outside of the work area to contain any debris.

The applicant would conduct project work at lower tides when the likelihood of creating turbid conditions is less. All removed piles, surface debris, and all containment supplies will be disposed of at a permitted upland disposal site. New riprap would be sourced from a local supplier. Old riprap would be disposed of in a local upland location.

Mitigation: The applicant proposes to avoid and minimize impacts from the project by proposing to complete all in-water work between November 1 and February 1, the preferred in-water work window for the Yaquina River estuary. Piling removal and installation will be conducted in accordance with the General Construction design criteria outline in the SLOPES IV In-water/Over-water Structures programmatic opinion. The existing creosote piles will be dislodged with a vibratory hammer and slowly lifted from the sediment and placed into a containment basin.

The contractor will initiate daily “soft-start” procedures to provide a warning and/or give marine mammals near pile driving and removal activities a chance to leave the area prior to a vibratory or impact driver operating at full capacity, thereby exposing fewer animals to loud underwater and airborne sounds. It is anticipated that all piles will be started with a vibratory hammer but will require impact driving for at least 10-20 feet due to required pile capacities and geologic conditions at this site. 

The applicant did not propose compensatory mitigation in the permit application. The Corps will determine the type and amount of compensatory mitigation necessary to offset environmental losses from the proposed project.

Drawings: Fourteen (14) drawings are attached and labeled Corps No. NWP-2019-545/2. Copies of this public notice, which have been mailed or otherwise physically distributed, feature project drawings in black and white. The electronic version features those drawings in color, which we think more accurately illustrates the proposed project. To access the electronic version of this public notice, go to the Portland District Regulatory website at and under Regulatory Pages select Permit Application Public Notices.

Authority: The proposed project will be evaluated under the following:

Section 10, Rivers and Harbors Act 1899 (33 U.S.C. 403), for work in or affecting navigable waters of the United States.

Section 14, Rivers and Harbors Act 1899 (33 U.S.C. 408) (referred to as “Section 408”), for work to alter a Corps civil works project. An alteration is defined as any action that builds upon, alters, improves, moves, occupies or otherwise affects the usefulness, or the structural or ecological integrity of a Corps federally authorized project. The proposed project may alter the Yaquina Bay Navigation channel. 
Section 404, Clean Water Act (33 U.S.C. 1344), for discharge of dredged or fill material into waters of the United States.

Clean Water Act Section 404(b)(1) Guidelines: The described discharge will be evaluated for compliance with guidelines promulgated by the U.S. Environmental Protection Agency under authority of Section 404(b)(1) of the Clean Water Act. The 404(b)(1) Guidelines are the substantive criteria used in evaluating discharges of dredged or fill material into waters of the United States. The source of the fill material would be a local supplier. 

Water Quality Certification: Section 401 of the Clean Water Act (33 U.S.C. 1341) requires applicants to obtain a water quality certification for proposed discharges into waters of the United States. A permit for the described work will not be issued until certification has been issued or is waived from the certifying state. The state’s notice for a water quality certification is attached.

Endangered Species: Section 7 of the Endangered Species Act (ESA) (16 U.S.C. 1536) requires federal agencies to consult with the National Marine Fisheries Service (NMFS) and/or U.S. Fish and Wildlife Service (USFWS) on all actions that may affect a species listed (or proposed for listing) under the ESA as threatened or endangered or that may adversely modify designated critical habitat. The Corps’ preliminary review indicates the described activity may affect an endangered or threatened species or designated critical habitat. The Corps has initiated consultation under Section 7 of the ESA. The Corps will complete the required consultation prior to finalizing a permit decision.

Essential Fish Habitat: Section 305(b)(2) of the Magnuson-Stevens Fishery Conservation and Management Act (MSA) as amended (16 U.S.C. 1855), requires Federal agencies to consult with the NMFS on all actions, or proposed actions, permitted, funded, or undertaken by the agency, that may adversely affect Essential Fish Habitat (EFH). The Corps’ preliminary review indicates the described activity would adversely affect EFH at the project location or in the vicinity. The Corps has initiated consultation under Section 305(b)(2) of the MSA. The Corps will complete the required consultation prior to finalizing a permit decision.

Historic Properties/Cultural Resources: Section 106 of the National Historic Preservation Act of 1966, as amended (54 U.S.C. 306108), requires Federal agencies to consult with the appropriate State and/or Tribal Historic Preservation Officer to take into account the effects of actions they undertake or permit on historic properties listed in or eligible for listing in the National Register of Historic Places. The Corps’ preliminary review indicates the described activity is not located on property registered or eligible for registration in the latest published version of the National Register of Historic Places. The proposed work is of such limited nature and extent that little likelihood exists for the proposed project to affect an unrecorded historic property or any other type of cultural resource.

State and Local Authorizations: The applicant has applied for the following additional governmental authorizations for the project: Removal-Fill Permit from the Department of State Lands (DSL) (DLS No. 62349-RF), Water Quality Certification from Department of Environmental Quality (DEQ) (Submittal # 22141), Estuarine Permit from City of Newport, Coastal Zone Consistency from Department of Land Conservation and Development (DLCD).

Public Hearing: Any person may request in writing within the comment period specified in this notice that a public hearing be held to consider this application. Requests for public hearings shall state with particularity the reasons for holding a public hearing.

Evaluation: The decision whether to issue a permit will be based on an evaluation of the probable impact, including cumulative impacts, of the described activity on the public interest. That decision will reflect the national concern for both protection and utilization of important resources. The benefit, which reasonably may be expected to accrue from the described activity, must be balanced against its reasonably foreseeable detriments. All factors, which may be relevant to the proposal will be considered including the cumulative effects thereof; among those are conservation, economics, aesthetics, general environmental concerns, wetlands, historic properties, fish and wildlife values, flood hazards, floodplain values, land use, navigation, shoreline erosion and accretion, recreation, water supply and conservation, water quality, energy needs, safety, food and fiber production, mineral needs, consideration of property ownership and, in general, the needs and welfare of the people.

The Corps is soliciting comments from the public; Federal, state, and local agencies and officials; Native American Tribes; and other interested parties in order to consider and evaluate the impacts of the proposed activity. Any comments received will be considered by the Corps to determine whether to allow an alteration of a federally authorized project or to issue, modify, condition, or deny a permit for this proposal. To make this decision, comments are used to assess impacts on endangered species, historic properties, water quality, general environmental effects, and the other public interest factors listed above. Comments are used in the preparation of an Environmental Assessment and/or an Environmental Impact Statement pursuant to the National Environmental Policy Act. Comments are also used to determine the need for a public hearing and to determine the overall public interest of the proposed activity.

Submitting Comments: Interested parties are invited to provide comments on the proposed project. Comments may be submitted by conventional mail or email. All comments received will be considered in determining whether authorizing the work would be contrary to the public interest. 

Either conventional mail or e-mail comments must include the Corps reference number as shown on page 1 and include the commenter’s name and address. In order to be accepted, e-mail comments must originate from the author’s e-mail account and must include on the subject line of the e-mail message the Corps reference number. All comments received will become part of the administrative record and are subject to public release under the Freedom of Information Act including any personally identifiable information such as names, phone numbers, and addresses.

Additional information about the proposed project may be obtained from the Corps Project Manager listed below. All comments, whether by conventional mail or email, must be received no later than the expiration date of this public notice to ensure consideration. Comments should be submitted to the following mailing address or email address:

        U.S. Army Corps of Engineers
        Brielle Cummings 
        Eugene Field Office
        211 E. 7th Avenue, Suite 105
        Eugene, Oregon 97401-2763
        Telephone: (503) 808-4387


Oregon Department of Environmental Quality (DEQ)
Water Quality 401 Certification

    Notice Issued: August 4, 2022
    Written Comments Due: September 3, 2022

Corps of Engineers No: NWP-2019-545/2
Oregon Department of State Lands No: 62349-RF    

WHO IS THE APPLICANT: Oregon State University, Scott Bond

LOCATION OF CERTIFICATION ACTIVITY: See attached U.S. Army Corps of Engineers public notice.

WHAT IS PROPOSED: See attached U.S. Army Corps of Engineers public notice on the proposed project.

NEED FOR CERTIFICATION: Section 401 of the Federal Clean Water Act requires applicants for Federal permits or licenses to provide the Federal agency a water quality certification from the State of Oregon if the proposed activity may result in a discharge to waters of the state.

DESCRIPTION OF DISCHARGES: See attached U.S. Army Corps of Engineers public notice on the proposed project.

WHERE TO FIND DOCUMENTS: Documents and materials related to water quality issues as a result of the proposal are available for examination and copying at Oregon Department of Environmental Quality, 401 Water Quality Permit Coordinator, Northwest Region, 700 NE Multnomah Street, Suite 600, Portland, Oregon 97232. Other project materials are available by contacting the Corps per the attached public notice.

Scheduling an appointment will ensure that water quality documents are readily accessible during your visit. To schedule an appointment please call DEQ Water Quality at Northwest Region at (503) 229-5623.

Any questions on the water quality certification process may be addressed to the 401 Permit Coordinator at (503) 229-5623 or toll free within Oregon at (800) 452-4011. People with hearing impairments may call the Oregon Telecommunications Relay Service at (800) 735-2900.


Public Hearing: Oregon Administrative Rule (OAR) 340-48-0032 (2) states that “The Corps provides public notice of and opportunity to comment on the applications, including the application for certification, provided that the department (DEQ), in its discretion, may provide additional opportunity for public comment, including public hearing.” Additional Section 401 process information is available on DEQ’s webpage (

Written comments: Written comments on project elements related to water quality must be received at the Oregon Department of Environmental Quality by 11:59 p.m. on the date specified in the upper right section on page one of this notice. Comments may be submitted electronically or through standard mail.

Electronic – Written comments may be submitted electronically through Your DEQ Online ( For questions regarding account registration, system navigation, or training resources, please visit the Your DEQ Online help webpage (

Mail – Oregon Department of Environmental Quality, Northwest Region
            700 NE Multnomah Street, Suite #600
            Portland, Oregon 97232
            Attn: 401 Water Quality Certification Coordinator

WHAT HAPPENS NEXT: DEQ will review and consider all comments received during the public comment period. Following this review, certification of the proposal may be issued as proposed, issued with conditions, or denied. You will be notified of DEQ’s final decision if you submit comments during the comment period. Otherwise, if you wish to receive notification, please call or write DEQ at the above address. Public records can be accessed through the Your DEQ Online public records portal webpage 

ACCESSIBILITY INFORMATION: DEQ can provide documents in an alternate format or in a language other than English upon request. Call DEQ at (800) 452-4011 or email