Water Protection Program fact sheet
Division of Environmental Quality Director: Ed Galbraith

For much of our history, many people thought wetlands were useless swamps filled with mosquitoes. Today, we know that wetlands are among the most productive ecosystems in the world, comparable to rain forests and coral reefs. A rich source of diversity, wetlands are home to a wide variety of plant and animal species that are crucial to a healthy environment.

Many species of birds and mammals rely on wetlands for food, water and shelter, especially during migration and breeding seasons. People depend on wetlands, too. Wetlands filter pollutants from our drinking water, provide natural flood control and help prevent our shorelines from eroding. Wetlands are an important part of our natural resources, worthy of our respect and deserving of our protection.

Unfortunately, more than half of the wetlands in the lower 48 states have already been lost as a result of drainage and filling. In its early history, Missouri had as much as 4.8 million acres of wetlands. By 1980, the number of wetlands in the state had dropped dramatically to 643,000 acres. Protecting and restoring our wetlands is one of today’s most critical environmental challenges.

Protecting wetlands

The federal government protects wetlands through regulations like Section 404 of the Federal Clean Water Act.

Section 401 of the Clean Water Act gives the states the authority to protect wetlands by regulating certain activities. Through the issuance of a Section 401 Water Quality Certification, the state ensures that a proposed project will not violate Missouri  water quality standards. Any activity involving the placement of dredged or fill material into waters of the state (including wetlands) must have a 401 certification from the department. Some of these activities might include the replacement of a low water stream crossing, construction of a levee, dams or dikes, and many other activities that require working below the ordinary high water mark of a stream. When a 401 certification is issued it becomes part of the 404 permit issued by the U.S. Army Corps of Engineers. 

If the Corps determines a 404 Permit is needed, a 401 Certification from the department is needed as well. The applicant of a 404/401 permit is required to avoid and/or minimize the project’s adverse impacts to wetlands and other waters of the state. If adverse impacts cannot be avoided, the department  will require compensatory mitigation for those impacts.

Applying for 401 Certification

Applying for a Section 401 Water Quality Certification is a two-step process.

  • Before you begin any project in a wetland, even those on your own property, it is crucial that you contact the U.S. Army Corps of Engineers. It will determine if you need a 404 Permit. There are two types of 404 permits: the Nationwide Permits, which belong to a larger group of general permits and are issued for proposed projects having minimal impacts to the environment; and Individual 404 permits issued to proposed projects having more than minimal impacts.  
  • If the Corps indicates the proposed project can be covered under a Nationwide Permit, it will issue the applicant an authorization letter that includes the conditions of the specified nationwide permit and the correlating 401 certification. If at any time a condition cannot be adhered to, the Corp and the department will need to be contacted. Certain nationwide permits or proposed projects will require an individual certification. This 401 certification generally takes no more than 60 days to be issued and requires a fee of $75.
  • If the Corps indicates you must apply for an individual 404 Permit, then you must also  apply to the department for an individual 401 Certification. The process involves conducting a public notice comment period on the proposed project. Upon receiving a complete application, the department has 60 days to respond to an official request for 401 certification. A fee of $75 is required upon completion of an individual 401 Certification.

For more information

U.S. Army Corps of Engineers - District Regulatory office phone numbers

Nothing in this document may be used to implement any enforcement action or levy any penalty unless promulgated by rule under chapter 536 or authorized by statute.

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