Wetlands Permitting (Section 401)

Laws of the United States and the State of Iowa have assigned the US Army Corps of Engineers (Corps) and the Iowa Department of Natural Resources (IDNR) with specific and different regulatory roles designed to protect the waters within and on the State's boundaries.

A Section 401 Water Quality Certificate is Iowa Department of Natural Resource's certification that a project will not violate state water quality standards and is required before the Corps of Engineers can issue a Section 404 permit.

Construction, excavation or filling in streams, lakes, wetlands, or on the flood plains may require permits from both the Corps and Iowa DNR. A Joint Application Form (Protecting Iowa Waters) shall be submitted to both agencies to begin the permit process for any of the following activities:

  • cutting the bank of a river, stream, or lake;
  • any excavation or dredging in a wetland, lake, stream or river;
  • channel changes or relocations (including stream straightening);
  • construction of any permanent dock, pier, wharf, seawall, boat ramp, beach, intake or outfall structure on a stream, river or lake;
  • placement of any fill, riprap, or similar material in a stream, river, lake, or wetland;
  • construction of a dam across any waterway;
  • placement of fill, construction of levees, roadways and bridges; and similar activities on a floodplain; or
  • construction of buildings on a flood plain.
  • Any construction on, above, or under all fee title lands and waters, dedicated lands and waters under the jurisdiction of the Natural Resource Commission (Commission) and managed by the Commission for public access to a meandered sovereign lake or meandered sovereign river; meandered sovereign lakes; meandered sovereign rivers; and sovereign islands (except those portions of the Iowa River and Mississippi River where title has been conveyed to Charter Cities). Sovereign Lands Construction Permit

The Iowa Department of Natural Resources also requires permits for the construction and operation of water and wastewater treatment facilities, water withdrawal, water storage, and solid waste disposal and should be contacted for information about these permits.

US Army Corps of Engineers:
Joint Application Form
Joint Application Form

Chapter 61: Water Quality Standards

US Army Corps of Engineers: Answers to Frequently Asked Questions
Rock Island District - Public Notices
Omaha District/DNR - Public Notices

Corps of Engineers & DNR Public Notices/Documents for Public Comment:

Public Comment Period for Section 401 Water Quality Certification for U.S. Army Corps of Engineers Reissued Nationwide Permits

The Iowa Department of Natural Resources (IDNR) is soliciting comments for the re-certification of the reissued U.S. Army Corps of Engineers (Corps) 2017 Nationwide Permits (NWPs). In accordance with the state and federal statutes and regulations, applicants seeking NWP authorization under Section 404 of the Clean Water Act from the Corps must also have a Clean Water Act Section 401 Water Quality Certification (WQC) for authorization to discharge to waters of the state. The proposed WQC has 3 new Iowa Regional Conditions to provide additional environmental protection for the 2017-2022 NWPs. The proposed WQC can be viewed below.

NWPs are general permits that authorize specific activities which involve the discharge of dredged or fill material into waters of the United States, including wetlands. Information regarding the 2017 NWPs can be viewed at http://www.usace.army.mil/Missions/Civil-Works/Regulatory-Program-and-Permits/Nationwide-Permits/

The Rock Island District Corps is also soliciting comments for the proposed Iowa Regional Conditions (see http://www.mvr.usace.army.mil/Missions/Regulatory/PublicNotices.aspx). The Corps’ public notice period ends on February 23, 2017. Comments to the Corps should be sent to District Engineer,

US Army Corps of Engineers, Rock Island District, ATTN: OD-P, Clock Tower Building- Post Office Box

2004, Rock Island, Illinois 61204-2004. Mr. Joey Shoemaker, Project Manager (309-794-5559), email:


IDNR staff will be available on Wednesday February 1, 2017 from 10:30 AM to 12:30 PM to answer any questions or accept comments regarding the WQC.  If interested, please go to the Wallace State Office Building at 502 E. 9thStreet, Des Moines, IA Conference Room 4W. Please stop at the front desk on the 4th floor to sign in and receive a visitor’s badge.

DATES: Submit your comments regarding the IDNR WQC by COB on February 27, 2017.

ADDRESSES: You may submit comments to the IDNR by any of the following methods:

E-mail: Christine.schwake@dnr.iowa.gov

Mail: Iowa Department of Natural Resources, Attn: Christine Schwake, 502 E. 9th Street, Des Moines, IA  50319-0034.

Fax: 515-725-8202 (Attention: Christine Schwake)

In person at the February 1, 2017 meeting

Please Note:  Comments on the WQC should be confined to the issues relating to the proposed WQC and the effect on water quality.

DNR Contact:  Christine Schwake, DNR, at Christine.Schwake@dnr.iowa.gov or 515-725-8399

Section 401 Water Quality Certification for the 2017 NWPs

Contact Information
Christine Schwake
Iowa Dept. of Natural Resources
Wallace State Office Building
502 E. 9th Street
Des Moines, IA 50319-0034
Phone: 515-725-8399
Fax: 515-725-8202
US Department of the Army, Rock Island
Rock Island District Corps of Engineers
Clock Tower Building - PO Box 2004
Rock Island, IL 61204-2004
Phone: 309-794-5376
Fax: 309-794-5191

US Department of the Army, Omaha
Omaha District Corps of Engineers
8901 South 154th Street
Omaha, NE 68138-3611
Phone: 402-896-0896


Outstanding Iowa Waters
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