Skip to main content

State level implementation

Stormwater programs and permit requirements

This section is intended to serve as guidance to assist stormwater practitioners and the regulated community in identifying and complying with existing federal, state, and local regulations. Local programs can vary considerably and go beyond the scope of this document to address individually, though several of the major programs implemented at a local level have been summarized here. Contact the local zoning authority for more specific information on requirements for the project area.

Contents

State level implementation

The following programs are implemented at the state level.

Stormwater Program

The Stormwater Program is a comprehensive state stormwater program based on the Federal NPDES program and administered by the MPCA with oversight by the USEPA. The program is based on federal Clean Water Act requirements for addressing polluted stormwater runoff. Stormwater disposal is regulated nationally through the National Pollutant Discharge Elimination System (NPDES) and Minnesota regulates the disposal of stormwater through the State Disposal System (SDS) MPCA issues combined NPDES/SDS permits.

A 1987 amendment to the Federal Clean Water Act required implementation of a two-phase comprehensive national program to address stormwater runoff. Phase I regulated large construction sites, 11 categories of industrial facilities, and major metropolitan municipal separate storm sewer systems (MS4s), including Minneapolis and St. Paul. Phase II includes smaller construction sites, municipally owned or operated industrial activity, and many more municipalities.

Stormwater permits require permittees to control polluted discharges. Regulated parties must develop stormwater pollution prevention plans (or stormwater pollution prevention programs, for Municipal Separate Storm Sewer Systems (MS4s)) to address their stormwater discharges. Each regulated party determines the appropriate best management practices (BMPs) to minimize pollution for their specific site. The three permit types - construction, industrial, and municipal - have distinct requirements and some regulated parties may require more than one permit.

There are two types of NPDES/SDS permits: general permits and individual permits. If work meets the requirements of a specific general permit, an individual permit is not required. Currently there are three categories for stormwater permitting as follows:

  1. Construction Stormwater Permitting Program. The Construction Stormwater Permitting Program is designed to reduce the amount of sediment and pollution entering surface and groundwater associated with construction projects. Prior to applying for permit coverage, the owner is required to develop a Stormwater Pollution Prevention Plan (SWPPP) that incorporates specific best management practices applicable to their site. Examples of construction activities requiring a permit include road building, landscaping clearing, grading, excavation, and construction of homes, office buildings, industrial parks, landfills and airports. Permits are required from owners and operators for any construction-related activity disturbing one acre or more of land. In some cases, smaller sites may require permit coverage if they are part of a larger common plan for development
  2. Industrial Stormwater Permitting Program. The Industrial Stormwater Permitting Program is designed to reduce the amount of pollution that enters surface and groundwater from industrial facilities in the form of stormwater runoff. Stormwater discharges associated with 11 categories of industrial activities are regulated. Industrial facilities require that a permit must develop and implement a SWPPP designed to eliminate or minimize stormwater contact with significant materials that may result in polluted stormwater discharges from the industrial site
  3. Municipal Stormwater Permitting Program. The Municipal Separate Storm Sewer System Stormwater (MS4) Permitting Program is designed to reduce the amount of sediment and pollution that enters surface and groundwater from storm sewer systems to the maximum extent practicable. Stormwater discharges associated with MS4s are regulated and the owners or operators of these systems are required to develop a SWPPP that incorporates best management practices applicable to their MS4. The most recent MS4 general permit is effective November 16, 2020 through November 16, 2025.
  4. Enabling Legislation: Section 404, Clean Water Act; Minnesota Statutes, Chapter 115; Minnesota Rules, Chapter 7001; Minnesota Rules, 7050; Minnesota Rules, Chapter 7090
  5. Required Permit(s): NPDES/SDS General Stormwater Permit for Construction; NPDES/SDS General Stormwater Permit for Industrial; NPDES/SDS General Stormwater Permit for Municipal Separate Storm Sewer Systems; NPDES/SDS Individual Stormwater Permit
  6. Regulatory Authority: Minnesota Pollution Control Agency; U.S. Environmental Protection Agency
  7. Applicability: Stormwater
  8. Stormwater Relationship: Stormwater discharge

Feedlot Program

The feedlot program regulates the collection, transportation, storage, processing and disposal of animal manure and livestock processing activities, and provides assistance to counties and the livestock industry. The rules apply to all aspects of livestock production areas including the location, design, construction, operation and management of feedlots, feed storage, stormwater runoff, and manure handling facilities.

There are two NPDES/SDS permits for feedlots: general permits for livestock production and individual permits for an animal feedlot or manure storage area. If the proposed facility meets the requirements of the general permit, an individual permit is not required. An individual permit is required if the proposed project does not meet the requirements of a specific general permit due to size or past infractions.

  1. Enabling Legislation: Clean Water Act; Minnesota Statutes, Chapter 115; Minnesota Rules Chapter 7020
  2. Required Permits: NPDES/SDS General Permit for Livestock Production; NPDES/SDS Permit for an Animal Feedlot or Manure Storage
  3. Regulatory Authority: Minnesota Pollution Control Agency; Counties; U.S. Environmental Protection Agency (oversight)
  4. Applicability: Feedlots
  5. Stormwater Relationship: Location, design, construction, operation and management of feedlots, feed storage, stormwater runoff, and manure handling facilities

Minnesota Impaired Waters and Total Maximum Daily Load (TMDL) Program

In compliance with Section 303 of the Clean Water Act, this program publishes an updated list of impaired waters every two years. An impaired water does not meet the water quality standards established to protect the designated use (i.e., fishing, swimming, irrigation, etc.) of those waters due to pollutants. The MPCA is required to conduct a TMDL study which identifies both point and nonpoint sources of each pollutant in and impaired water that fails to meet water quality standards. A TMDL specifies the maximum amount of a pollutant that a waterbody can receive and still meet water quality standards, and allocates pollutant loadings among point and nonpoint pollutant sources

  1. Enabling Legislation: Clean Water Act, Section 303; Minnesota Statutes, Chapter 115; Minnesota Rules, Chapter 7052
  2. Required Permit(s): Compliance with a TMDL plan, once adopted by MPCA
  3. Regulatory Authority: Minnesota Pollution Control Agency; U.S. Environmental Protection Agency (oversight)
  4. Applicability: Impaired waters
  5. Stormwater Relationship: Discharges to impaired waters
  6. Stormwater Relationship: Stormwater discharge to an impaired water or a water with a TMDL.

Section 401, Water Quality Certification

Anyone who wishes to obtain a federal permit for any activity that may result in a discharge to a navigable water must first obtain a state 401 water quality certification. This program requires the applicant to demonstrate that a proposed activity will not violate Minnesota’s water quality standards or result in adverse long-term or short-term impacts on water quality. Such impacts can be direct or cumulative with other indirect impacts. Because MPCA staff is no longer assigned to evaluate 401 applications for conformance with water-quality standards, the MPCA has decided to waive its 401 authority in most, but not all, cases. However, this should not be viewed as a waiver from the requirements of MN Rule, Chapter 7050. This action does not waive MPCA’s authority to take necessary enforcement actions to ensure that the applicant and the project’s construction, installation, and operation comply with water quality standards, statutes and rules.

  1. Enabling Legislation: Clean Water Act, Section 401; Minnesota Statutes, Chapter 115; Minnesota Rules, Chapter 7001
  2. Required Permit: Section 401 Water Quality Certification or Waiver
  3. Regulatory Authority: Minnesota Pollution Control Agency; U.S. Environmental Protection Agency (oversight)
  4. Applicability: Waters of the U.S.; Waters of the State
  5. Stormwater Relationship: Discharge of stormwater or alteration of wetland in violation of state water quality standards

Nonpoint Source Management Program and Coastal Nonpoint Source Pollution Control Program

Section 319 of the Clean Water Act requires each state to address nonpoint pollution by developing nonpoint source assessment reports that identify nonpoint source pollution problems and the nonpoint sources responsible for the water quality problems. States also adopt management programs to control nonpoint source pollution and then implement the management programs. States, Territories, and Indian Tribes can receive Section 319 grant money which supports a wide variety of activities including technical assistance, financial assistance, education, training, technology transfer, demonstration projects, and monitoring to assess the success of specific nonpoint source implementation projects

Minnesota became part of the national Coastal Management Program after receiving federal approval in July 1999. Minnesota’s Lake Superior Coastal Nonpoint Pollution Control Program is designed to reduce nonpoint pollution in the Lake Superior Basin.

  1. Enabling Legislation: Section 319, Clean Water Act
  2. Required Permit(s): NA
  3. Regulatory Authority: Minnesota Pollution Control Agency; U.S. Environmental Protection Agency (oversight)
  4. Applicability: Waterbodies, streams, and associated uplands; Lake Superior Basin
  5. Stormwater Relationship: Nonpoint sources of pollution

Drinking Water Protection Program

This program’s mission is to protect the public health by ensuring a safe and adequate supply of drinking water at all public water systems (community and non-community drinking water systems). The program reviews plans for water system improvements, conducts on-site inspections and sanitary surveys, provides training and technical assistance, ensures that water systems are tested for contaminants, and takes action against water systems not meeting standards.

  1. Enabling Legislation: Safe Drinking Water Act; Minnesota Statutes, Chapter 103H; Minnesota Rules Chapter 4720
  2. Required Permit: NA
  3. Regulatory Authority: Minnesota Department of Health
  4. Applicability: Public drinking water systems and their source areas
  5. Stormwater Relationship: Source water contamination

Source Water Protection Program

This program applies to drinking water and its sources, which includes rivers, lakes, reservoirs, springs, and ground water wells. The Source Water Protection Program’s purpose is to help prevent contaminants from entering public drinking water sources. There are three different classifications of public water systems: communities, transient noncommunities, and nontransient noncommunities. For groundwater supply areas, each of the public water system categories maintains an inner wellhead management zone, which is a 200-foot radius around wellsIn addition, communities and nontransient noncommunities must also identify capture zones for their wells (wellhead protection areas) and create a formal wellhead protection plan

The Source Water Protection Program consists of three primary parts:

  1. Wellhead Protection Program: The purpose of the Wellhead Protection Program is to prevent contamination of public drinking water supplies by identifying water supply recharge areas and implementing management practices for potential pollution sources found within those areas
  2. Source Water Assessment Program: The purpose of the Source Water Assessment Program is to develop reports that provide a concise description of the water used by a public water system and identify susceptibility to contamination

  3. Surface Water Intake Protection: Protection for surface water intakes is not required, but many of Minnesota’s community water supply systems that use surface water have expressed interest in developing protection plans.

     

The Minnesota Department of Health is currently developing guidelines for protection plans.

  1. Enabling Legislation: Minnesota Statutes, Chapter 103H; Minnesota Statutes, Chapter 103I; Minnesota Statutes, Chapter 144; Minnesota Rules, Chapter 4720; Minnesota Rules, Chapter 4725
  2. Required Permit: NA
  3. Regulatory Authority: Minnesota Department of Health
  4. Applicability: Source waters for public drinking water systems
  5. Stormwater Relationship: Source water contamination

Public Waters Work Permit Program

This program, begun in 1937, regulates water development activities below the ordinary high water level (OHWL) in public waters. The Public Waters Work Permit Program applies to those lakes, wetlands, and streams identified on DNR Public Water Inventory maps. Proposed projects affecting the course, current, or cross-section of these water bodies may require a Public Waters Work Permit from the DNR.

There are two types of Public Waters Work Permits: general permits and individual permits. If work proposed in public waters or public waters wetlands meets the requirements of a specific general permit, an individual permit is not required. Currently there are five categories of general permits.

  1. Emergency Repair of Public Flood Damages
  2. Multiple Purposes
  3. Bridge and Culvert Projects
  4. Dry Hydrants
  5. Bank/Shore Protection or Restoration

An individual permit is required if the proposed work does not meet the requirements of a specific general permit. There are also deregulated activities for which no permit is required.

  1. Enabling Legislation: Minnesota Statutes 103G; Minnesota Rules Chapter 6115
  2. Required Permit(s): Public Waters Work Permit
  3. Regulatory Authority: DNR, Division of Waters
  4. Applicability: Activities below the ordinary high water level (OHWL) in designated public waters
  5. Stormwater Relationship: Filling, excavation, shore protection, bridges, culverts, structures, docks, marinas, water level controls, dredging, dams or other activities affecting the course, current or cross section.

Water Appropriations Permit Program

This program was created in response to legislation requiring DNR to balance competing management objectives that include both development and protection of Minnesota’s water resources. The Water Appropriations Permit Program applies to all users withdrawing more than 10,000 gallons of water per day or 1 million gallons per year. Proposed projects withdrawing this amount of water or more may require a Water Appropriations Permit from the DNR.

There are several types of water appropriations permits including general permits and individual permits for both irrigation and non-irrigation purposes. Several exemptions apply for domestic uses serving less than 25 people, test pumping of a groundwater source, reuse of water already authorized by a permit, and for certain agricultural drainage systems. If appropriations meet the requirements for one of the general permits then an individual permit is not required.

Currently there are two categories of general permits.

  1. Temporary Projects: authorizes temporary water appropriations for construction dewatering, landscaping, dust control, and hydrostatic testing of pipelines, tanks, and wastewater ponds.
  2. Animal Feedlots and Livestock Operations: authorizes groundwater appropriations up to 5 million gallons per year for livestock watering and sanitation purposes.

If the proposed appropriation does not meet the requirements of a specific general permit or is not exempt, an individual permit is required.

  1. Enabling Legislation: Minnesota Statutes, Section 103G65; Minnesota Rules Chapter 6115
  2. Required Permits: Water Appropriations Permit
  3. Regulatory Authority: DNR, Division of Waters
  4. Applicability: Surface and ground water withdrawals greater than 10,000 gallons of water per day or one million gallons per year
  5. Stormwater Relationship: Discharge of water withdrawals.

Calcareous Fen Protection

Calcareous fens are classified as outstanding resource value waters (ORVWs) and are protected under the restricted discharge provisions of the MPCA water quality standards in Minnesota Rule 7050.0180 Subp6. In addition, calcareous fen protections were also put in place in 1991 with the passing of the Wetland Conservation Act and regulate activities that may alter or degrade calcareous fens. Calcareous fens are the rarest wetland community in Minnesota and may not be drained or filled or otherwise altered or degraded except as provided for in a management plan approved by the commissioner.

  1. Enabling Legislation: Clean Water Act, Section 401; Minnesota Statutes, Section 103.G23; Minnesota Statutes, Section 115; Minnesota Rules Chapter 7001; Minnesota Rules Chapter 7050; Minnesota Rules Chapter 8420; Commissioner’s Order No05-001
  2. Required Permits: Approved Calcareous Fen Management Plan; NPDES/SDS General Stormwater Permit
  3. Regulatory Authority: Minnesota Department of Natural Resources; Minnesota Pollution Control Agency
  4. Applicability: Calcareous fens
  5. Stormwater Relationship: Drainage, fill, alteration, or degradation of a calcareous fen

Dam Safety Program

This program was created in 1978 in response to the federal Dam Safety Act and regulates the repair, operation, design, construction, and removal of public and private dams. The program sets minimum standards for dams regarding safety, design, construction, and operation and it classifies dams into three dam hazard classes. Proposed projects for construction, alteration, repair, removal or transfer of ownership of a regulated dam may require a Public Waters Work Permit.

  1. Enabling Legislation: Dam Safety Act; Minnesota Statutes, Section 103G.515; Minnesota Rules, parts 6115.0300 through 6115.0520
  2. Required Permits:

Public Waters Work Permit

  1. Regulatory Authority: DNR, Division of Waters
  2. Applicability: Structures that pose a potential threat to public safety or property. Dams 6 feet high or less and dams that impound 15 acre-feet of water or less are exempt from state dam safety rules as are dams that are less than 25 feet high and impound less than 50 acre-feet, unless there is a potential for loss of life due to failure or mis-operation.
  3. Stormwater Relationship: Repair, operation, design, construction, and removal of regulated dams

Mississippi River Critical Area Program

The Mississippi River Critical Area Program is a joint local and state program that provides coordinated planning and management for 72 miles of the Mississippi River, four miles of the Minnesota River, and 54,000 acres of adjacent corridor lands.

  1. Enabling Legislation: Minnesota Statutes, Section 116G; Minnesota Rules, Chapter 4410
  2. Required Permits: NA
  3. Regulatory Authority: DNR, Division of Waters; Local Government
  4. Applicability: Sections of the Mississippi and Minnesota River and designated corridor
  5. Stormwater Relationship: Activities within the critical area

Wild and Scenic Rivers Program

In Minnesota, the Department of Natural Resources maintains the state Wild and Scenic River Program and cooperates with the Wisconsin Department of Natural Resources and the National Park Service for management of the lower St. Croix River, which is part of the National Wild and Scenic Rivers Program. The purpose of the Wild and Scenic Rivers Programs is to preserve select rivers with outstanding scenic, recreational, geologic, fish and wildlife, historic, cultural or other important values in a free-flowing condition.

Six rivers in Minnesota have segments, which are designated as wild, scenic, or recreational under the state program in addition to the federally designated lower St. Croix River. These rivers are also designated as Outstanding Resource Value Waters (ORVWs) in Minnesota. Each of the designated river segments in Minnesota has a management plan, which outlines the rules and goals for that waterway. These rules work together with local zoning ordinances to protect the rivers from pollution, erosion, over-development, and degradation factors, which undermine the wild, scenic, and recreational qualities for which they were designated

  1. Enabling Legislation: National Wild and Scenic Rivers Act; Minnesota Statutes, Chapter 103F; Minnesota Rules, Chapter 6105
  2. Required Permit: Compliance with management plan for the river
  3. Regulatory Authority: DNR, Division of Waters; National Park Service; Local Government
  4. Applicability: Portions of the St. Croix River, Mississippi River, Kettle River, Rum River, North Fork of the Crow River, Minnesota River, and Cannon River
  5. Stormwater Relationship: Restrictions on activities adversely affecting the river or its designated corridor.

Lake Superior Coastal Program

Minnesota participates in the federal Coastal Zone Management program through the Lake Superior Coastal Program. Local issues that the program helps to address include: shoreline erosion, inadequate sewage and stormwater systems, local watershed and land use planning, habitat restoration, waterfront revitalization, and water access. The program was developed to encourage greater cooperation, to encourage simplification of governmental processes, and provide tools to implement existing policies, authorities and programs within the area defined by the program boundary. Lake Superior is designated as an ORVW in Minnesota.

  1. Enabling Legislation: Coastal Zone Management Act of 1990, Section 6217
  2. Required Permit(s): NA
  3. Regulatory Authority: DNR, Division of Waters US Environmental Protection Agency; National Oceanic and Atmospheric Administration
  4. Applicability: Coastal Zone of Lake Superior
  5. Stormwater Relationship: Discharges adversely impacting land and water resources within the designated coastal zone

National Flood Insurance Program

The National Flood Insurance Program (NFIP) enables property owners in participating communities to purchase insurance protection against losses from flooding. Participation in the NFIP is based on an agreement between local communities and the federal government that states if a community will adopt and enforce a floodplain management ordinance to reduce future flood risks to new construction in Special Flood Hazard Areas, the federal government will make flood insurance available within the community as a financial protection against flood losses. In Minnesota, the National Flood Insurance Program is administered by the Minnesota Department of Natural Resources. By state law, all flood prone communities in the state are required to participate in the program.

  1. Enabling Legislation: National Flood Insurance Act of 1968
  2. Required Permit(s): NA
  3. Regulatory Authority: DNR, Division of Waters; Federal Emergency Management Agency; Local Government
  4. Applicability: Flood-prone communities
  5. Stormwater Relationship: Restrictions on activities and structures in floodplain

Utility Crossing License Program

This is a licensing program for the passage of any utility over, under or across any state land or public waters.

  1. Enabling Legislation: Minnesota Statutes, Chapter 84; Minnesota Rules, Chapter 6135
  2. Required Permit: Utility Crossing License
  3. Regulatory Authority: DNR, Department of Land and Minerals
  4. Applicability: Public waters or state land
  5. Stormwater Relationship: Utility crossings of public waters or state land

Comprehensive Local Water Management

The Board of Water and Soil Resources (BWSR) oversees the adoption and implementation of comprehensive local water management plans, which are voluntary plans created by counties outside the seven-county metropolitan area. The Act, passed in 1985 encourages counties outside the metropolitan area to protect water resources through the adoption and implementation of local water management plans that are based on local priorities.

  1. Enabling Legislation: Minnesota Statutes 103B.301
  2. Required Permit(s): NA
  3. Regulatory Authority: Board of Water and Soil Resources; Local Government
  4. Applicability: Counties outside the seven-county metro area
  5. Stormwater Relationship: Erosion and sedimentation reduction, storm water design standards, wetland protection

Comprehensive Surface Water Management

The Board of Water and Soil Resources oversees the adoption and implementation of comprehensive surface water management plans, which are created by watershed districts, watershed management organizations, or county/city/township joint powers organizations within the seven-county metropolitan area

After local, regional, and agency review, plans are approved by the Board of Water and Soil Resources. The WMO/WD/JPO then formally adopts the plan and requires each city or township within the WMO/WD/JPO to create and implement their own local water management plan consistent with the WMO/WD plan. Updates are required every 5-10 years.

  1. Enabling Legislation: Minnesota Statutes 103B; Minnesota Rules Chapter 8410
  2. Required Permit(s): NA
  3. Regulatory Authority: Board of Water and Soil Resources; Local Government
  4. Applicability: Watershed Districts, Water Management Organizations, or Joint Powers Organizations in seven-county metro area
  5. Stormwater Relationship: Erosion and sedimentation reduction, storm water design standards, wetland protection