Clean Water Act Section 401 Water Quality Certifications

401 Certifications for Section 404 Regional General Permits and Nationwide Permits

Role of Section 401 water quality certification

The 401 certification is part of a larger water quality protection effort that is an integral part of the federal Clean Water Act. In Minnesota, other agencies also play a role in water quality protection: the Minnesota Department of Natural Resources (DNR), the Minnesota Board of Soil and Water Resources (BWSR), and local government agencies.

The MPCA 401 Certification fills a unique niche in protecting water quality by applying state water quality standards to projects.

What activities require a Section 401 water quality certification?

Section 401 of the Clean Water Act requires any applicant for a federal license or permit to conduct an activity that may result in a discharge of a pollutant into waters of the United States to obtain a certification from the State in which the discharge originates that the discharge complies the applicable water quality standards. The 401 certification becomes a condition of Federal permits including Coast Guard Section 10 permits, Federal Energy Regulatory Commission (FERC) permits and U.S. Army Corps of Engineers (Corps) Section 404 permits.

For example, if someone proposes to place dredged or fill material into navigable waters of the U.S., including wetlands, they must obtain a Section 404 permit from the U.S. Army Corps of Engineers and a Section 401 water quality certification from the Minnesota Pollution Control Agency (MPCA). The Section 404 Corps permit is by far the most common federal permit issued in Minnesota that requires a Section 401 determination from the MPCA.

How long does it take to receive a 401 water quality certification?

The vast majority of 401 activities involve projects with relatively low risk to water quality. These are regulated by federal 404 general permits and related 401 certifications The MPCA certifies these general permits and no individual 401 certification is required for projects regulated by federal general permits. About 2,000 projects are authorized annually through general permits. The turnaround time for a 401 certification for a general permit is zero days because the activity has been pre-certified.

However, activities representing more significant risk to water quality are regulated through individual permits. About 50 Individual Permits are issued annually. The average turnaround time for MPCA certification of individual permits is about 90 days. Examples of higher risk projects include:

  • Mining operations
  • Dam removal
  • Large bridges
  • Large pipeline and transmission lines

The MPCA is committed to meeting turnaround time goals set by the Governor and Legislature. Every effort is made to quickly review applications and provide feedback regarding missing information and make a final determination as soon as possible and well within established goals.

Outstanding Resource Value Waters

Waters designated as Prohibited Outstanding Resource Value Waters or Restricted Outstanding Resource Value Waters (ORVW) have an extra level of protection associated with them to protect their unique nature. Any projects proposed in a Prohibited ORVW must apply for an individual 401 Water Quality Certification. Any project in a Restricted ORVW may be required to apply for an individual 401 Water Quality Certification. Refer to Minn. R. 7050.0335 for a list of Prohibited and Restricted ORVWs or use the interactive map below to determine if your project has potential to impact a Restricted or Prohibited ORVW.

This map does not include fens, which are typically regulated through DNR fen Management plans and do not require additional regulation through the 401 Water Quality Certification Program.

Helpful hints

The MPCA is committed to providing both fast and value-added 401 certifications. Although the MPCA does not consider 401 Certifications to be a permit, we have agreed to follow the Governor's Executive Order regarding turnaround times. The MPCA turnaround time for 401 certification is about 90 days for Individual Permits. The MPCA also typically provides feedback on application information within 30 days, after the receipt of the Wetland Application.

The MPCA recognizes that project applicants must work with a number of units of government to secure overall approval to proceed. With this in mind, we focus our reviews on the intended legal purpose of our certification; compliance with water quality standards. For many projects, risk to water quality is low. These projects are either pre-certified through the general permit or are individual permits which are waived.

However, every year there several projects which potentially threaten water quality and are the focus of the MPCA's 401 Certification water quality protection efforts. Examples of projects of this nature include:

  • Large amounts of wetland filling which alter the hydrology and biology of a watershed and increase the likelihood of damaging water quality. If these projects also involve wetland replacement outside the watershed or water basin, they are especially of concern.
  • Direct filling of significant areas of lakes or streams in a manner that affects water quality.
  • Projects impacting waters designated by rule as outstanding resource value waters as defined in Minn. R. 7050.0180 or any cold water designated stream or lake.

If a project applicant has a project involving one of these 4 scenarios, we advise calling MPCA early in your project planning to discuss water quality issues and keep your project moving forward. Resolving issues early will prevent problems and possible project delays.

How do I apply for a Section 404 permit and a Section 401 certification?

Click on the Joint Application Form link below, fill out and submit to the U. S. Army Corps of Engineers (Corps). The link provided in the Joint Application Form will direct you to the appropriate Corps contact for submittal. Small projects, may quality for the Corps General Permit. If the project qualifies for a Corps General Permit, the MPCA has pre-certified and no further certification action by the MPCA is required. Larger projects will require a Corps Individual Permit. The Corps will use the application information to develop a public notice that in most cases can also be used as the MPCA’s public notice. However, in some cases the MPCA will be required to do its own public notice and will request additional information from the applicant.

More information

Jim Brist
Resource Management and Assistance Division
520 Lafayette Road North
St. Paul, MN 55155
Phone: 651-757-2245
Fax: 651-297-8676