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401 Water Quality Certification Program

Construction activities occurring in Illinois waterways, floodplains and wetlands often require both State and federal authorization. Anyone proposing to construct, operate or maintain any dam, dock, pier, wharf, sluice, levee, dike, building, roadway, utility crossing , piling, wall, fence or other structure in, or dredge, fill or otherwise alter the bed and banks of any stream, lake, wetland, floodplain or floodway subject to State and federal regulatory jurisdiction may be required to obtain approvals from the Illinois EPA and other state, federal or local authorities. Primarily, the U.S. Army Corps of Engineers and the Illinois Department of Natural Resources Office of Water Resources (IDNR/OWR) are involved in permitting of such construction activities. Further information on these agencies can be found at the Corps Regulatory websites provided below, or IDNR/OWR webpage here.

Program Overview

The Illinois EPA (Agency) issues water quality certifications pursuant to Section 401 of the federal Clean Water Act (CWA). This certification must be granted or waived prior to issuance of any federal permit that authorizes a potential discharge of dredged or fill material to a waters of the U.S. The Illinois EPA may also deny certification, which means that a federal permit cannot be issued.

CWA Section 401 specifies that the Agency must determine whether the proposed activities would meet federal and state water quality standards and other state water quality requirements.  The Agency's technical review focuses on potential impacts to water quality caused by the proposed construction or alteration of the waterbody but may also consider long term water quality impacts resulting from the facilities installation. A CWA Section 401 certification granted by the Agency may contain conditions and monitoring requirements deemed necessary to assure compliance with water quality standards or other applicable requirements. Conditions placed in the certification become conditions of the federal permit.

2026 Nationwide Permit 401 Certifications

The most common federal permit that requires Illinois EPA’s involvement with CWA Section 401 is the dredge and fill permitting program implemented by the U.S. Army Corps of Engineers (“Corps”) and authorized by CWA Section 404. Corps implements general permitting procedures to handle most of the permitting requirements that are characterized as having minimal adverse impacts.  The Illinois EPA issues blanket water quality certifications to Corps to help authorize these types of activities based on the premise of minimal adverse impacts.  A general permit with blanket certification is distinguished from a general permit with individual certification or an individual permit with individual certification. An individual certification is one that is issued to a specific applicant after a case-specific review has been conducted. The main type of federal general permit is the Nationwide Permit Program. Links to the Corps program and additional information regarding our water quality certifications and specific procedures are provided below.

Statutory and Regulatory Authorities

Section 401 Application Guidelines

Federal regulations at 40 CFR 121 have been implemented over the past few years and have significantly affected Illinois EPA’s implementation of the CWA Section 401 program. While the CWA prescribes that a certifying agency shall have no more than one year to act on a certification request, 40 CFR 121 adds additional requirements for the state to adhere to a more stringent reasonable period of time for making final determinations. The federal regulations also impose a pre-filing meeting request period of 30-days onto applicants. The Illinois EPA has incorporated these federal requirements into its procedures. The application requirements will be transmitted via email notification to the applicant for a prefiling meeting request. Additional application instructions will also be provided in the Agency’s pre-file notification. The objective for the pre-filing process is to clarify for the applicant, what information will be necessary for submittal of the “Certification Request” If necessary, an actual meeting may be scheduled with Permit Section staff of the Division of Water Pollution Control; however, if an applicant carefully reads the notification letter, most of the typical questions will be readily answered. To adhere to the federal requirements, a "Pre-filing Meeting Request” must be initiated by the Applicant through submittal of the following:

Individual Certification Request Validation

In accordance with federal rules at 40 CFR 121 and Illinois EPA’s procedures, a certification request must consist of the information  

  1. Verification documentation that the federal agency has determined that the project requires State 401 certification or description of the specific reasons that an appliable general permit does not include blanket water quality certification. (see below).
  2. Technical information, to the extent necessary as determined in the Pre-filing stage.

For an application to be considered a valid certification request, the above items must be submitted as a package to the Agency. The verification documentation must contain unambiguous written confirmation from a federal agency's representative that an individual (case-specific) Section 401 water quality certification is required from the State of Illinois. The Agency will notify both the applicant and the person representing the federal agency of the date of the Agency's receipt of a valid certification request and it will advise of its findings regarding reasonable period of time necessary to complete its review.

If the Agency determines that a submittal is not a valid certification request, the Agency will send an email notification to interested parties that the submittal is not a valid certification request. The Applicant must correct the deficiencies noted in the notification letter and make a written submittal to obtain a valid certification request notification. The submittal date of the certification request, or resubmittal date, in the case that it was previously determined to be invalid, becomes the date that the reasonable period of time begins. 

Information Requirements

An Illinois EPA Section 401 certification review includes an evaluation of any data or information that the Illinois EPA determines to be necessary to reach a final determination pursuant to Section 401 of the federal CWA. This information includes but is not limited to requirements in the Illinois Pollution Control Board’s rules promulgated to comply with federal antidegradation policy, water quality standards, and effluent limitations as well as material testing requirements found in Title 35, Illinois Administrative Code, Subtitle C. Please call the Agency at 217/782-3362 for additional information.

Who Must Apply

If you still have questions about whether your project needs a case-specific 401 water quality certification, you should first contact the federal agency that has jurisdiction over your project. Most construction activities primarily fall under the jurisdiction of the U.S. Army Corps of Engineers (Corps) CWA Section 404 authority which regulates discharges of dredged or fill material to a waters of the U.S.  If you need assistance with information regarding the Corps' Nationwide Permits or other general 404 permit programs and blanket water quality certification applicability, please contact the appropriate Corps regulatory district. There are five (5) regulatory districts with jurisdiction in Illinois listed below:

Where to Apply, Fees, and What to Expect

A pre-filing meeting request may be submitted electronically via mail to the Illinois EPA at epa.401.bow@illinois.gov or at the addresses provided below. A submittal for individual certification request should be submitted at the address below and electronically.

A certification fee is required under Section 12.6 of the Act. The Agency cannot grant a certification without payment of the certification fee. While non-payment of the certification fee at the time of certification request is not alone a reason for deeming the certification request invalid, the Agency may deny certification if the fee is not paid by the earliest of either the 60th day prior to expiration of the reasonable period of time or when the Agency is ready to publish the public notice. The Illinois EPA is not able to refund certification fees paid. 

Water Quality Certification Fees

If additional information is needed by the Agency to complete its review and publish its findings in a public notice, the Agency may contact the applicant for additional technical information.

    Illinois EPA

    Attn: BOW Permit Section - 401/Mines

    2520 West Iles Avenue

    P.O. Box 19276

    Springfield, Illinois 62794-9276

Other Permits

Your construction project may also require authorization or a permit under other Illinois EPA permit programs, some of which are listed below. Permits are also required for construction and operation of drinking water facilities and related infrastructure. If you have any questions about these programs, please contact the Agency at 217 782-0610 or find out more at the Water Pollution Control Permit webpage.

Important Links

Section 401 Water Quality Certification Notices and Hearings