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 IDNR. 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.

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.