image showing overlap between jurisdictions of different agencies, including the Minnesota DNR (public waters), Minnesota Department of health (source water), Board of Water and Soil Resources (BWSR), and U.S. Army Corps of Engineers (waters of the U.S.)
Image showing overlap between jurisdictions of different agencies, including the Minnesota DNR (public waters), Minnesota Department of health (source water), Board of Water and Soil Resources (BWSR), and U.S. Army Corps of Engineers (waters of the U.S.)
Information: This page contains numerous references to federal, state, regional, and local agencies. Links to websites for these agencies can be found in the References section.

Many agencies at the federal, state, watershed, and local levels have jurisdiction over surface and ground waters in Minnesota. These jurisdictions can vary and overlap. Multiple agencies involved in managing the same jurisdictional water lead to complex regulations and permitting programs. This complexity is documented in the 2002 report by the Minnesota Planning Department titled: Charting a Course for the Future: Report of the State Water Program Reorganization Project.

This page focuses solely on those programs and permits that are specifically tied to stormwater management, though many other programs may exist that have an indirect stormwater connection. Examples include federal and state hazardous waste management, aboveground and underground storage tanks, solid waste management, oil handling and spill prevention, pesticide management, and facility planning and construction. (See also File:Issue paper C - stormwater regulatory framework.pdf)

This page focuses primarily on description/interpretation of programs and permits at the federal and state levels. Most of the decisions about development and land use however are made at the local level. It is also at the local level that the effects of runoff problems become most apparent and the responsibility for implementing and maintaining the stormwater infrastructure and stormwater management resides. Because of this, many of the federal and state regulatory programs have a large impact on stormwater management responsibilities at the local level. Counties, watershed organizations, regional agencies (e.g. Metropolitan Council), municipalities, and townships are all examples of local government groups that may have responsibility for stormwater management.

The implementation vehicle for many local stormwater management programs is through local ordinances. Stormwater management activities may be addressed through specific stormwater ordinances, zoning ordinances or development ordinances and may contain requirements for water quantity, water quality, erosion and sediment control, nonpoint source pollution control, channel protection, and natural area protection.

While the Manual has no regulatory authority in and of itself, it seeks to provide a sound technical basis for stormwater management design and implementation. This can be coordinated on a statewide level through existing laws and regulations. The following table provides a summary of regulatory authorities for some common stormwater management activities. It outlines the agencies with permitting or review authority and those with the ability to set standards or provide enforcement for those programs.

Summary of regulatory authorities for some federal, state and local agencies and government units.
Link to this table

Action classes
Federal
State
Locala
USEPA USACE FEMA MPCA DNR BWSR MDH Met Council LGUs
Erosion and sediment control Conditional Full Review Full
Lake, stream, river protection Conditional Full Review Full Full Review review Conditional
Wetland protection Review Full review Full FullReview Review Full
Groundwater protection Conditional Full Full Conditional Conditional Full
Surface water quality protection Conditional Full Conditional Review Review Conditional
Construction stormwater discharge Conditional Full Conditional Review Conditional
Municipal stormwater discharge Conditional Full Review Conditional
Industrial stormwater discharge Conditional Full Conditional Conditional
Agricultural stormwater discharge Conditional Full Review Conditional
Flood control Full Full Conditional Review Conditional

aDepending upon location in the state, the local jurisdictions may be administered at the county, watershed organization (if one exists), city/township/village, or tribal level, or a combination of these. contact the local zoning authority for more information on local regulations.
USEPA = United States Environmental Protection Agency, USACE = United States Army Corp of Engineers, FEMA = Federal Emergency Management Agency, MPCA = Minnesota Pollution Control Agency, DNR = Minnesota Department of Natural Resources, BWSR = Board of Water and Soil Resources, MDH = Minnesota Department of Health
Note: FEMA, BWSR and MDH have no enforcement authority for any of these action classes. Met Council has enforcement authority for industrial stormwater discharges. The remaining agencies have enforcement authority.


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.

Federal level implementation

The following programs are implemented at the federal level.

Section 404 permit program

This program applies to all waters of the United States, including lakes, rivers, ponds, streams, and wetlands. The Section 404 program regulates the discharge of dredged or fill material into waters of the U.S.

There are several categories of permits and approvals, including

  • non-reporting general permit;
  • statewide general permits;
  • letters of permission; and
  • individual permits.

An individual permit is required if the proposed work does not meet the requirements of one of the following specific general permits or letter of permission.

  1. Enabling Legislation: Section 404, Clean Water Act
  2. Required Permit: Section 404 Permit
  3. Regulatory Authority: U.S Army Corps of Engineers; U.S Environmental Protection Agency
  4. Applicability: Waters of the U.S.
  5. Stormwater Relationship: Discharge of dredged or fill material into waters of the U.S

Rivers and Harbors Act, Section 10 Permit Program

The Section 10 program applies to all Navigable Waters of the U.S. Navigable Water designation is based on past, present or potential use for transportation or interstate commerce. The Section 10 program regulates any work in, over or under a Navigable Water of the U.S or work that affects the course, location, condition or capacity of such waters.

There are several categories of permits and approvals, including

  • non-reporting general permit;
  • statewide general permits;
  • nationwide general permits;
  • letters of permission; and
  • individual permits.

An individual permit is required if the proposed work does not meet the requirements of one of the following specific general permits or letter of permission

  1. Enabling Legislation: Section 10, Rivers and Harbors Act
  2. Required Permit: Section 10 Permit
  3. Regulatory Authority: U.S. Army Corps of Engineers
  4. Applicability: Navigable Waters of the U.S
  5. Stormwater Relationship: Work in, over, under, or affecting the course, location, condition or capacity of a Navigable Water of the U.S

Underground Injection Control Program (Class V Injection Wells)

This program applies to shallow disposal systems that are used to place a variety of fluids, including stormwater, below the land surface. Class V injection wells are defined as any bored, drilled, driven shaft, or dug hole that is deeper than it is wide; any improved sinkhole; or any subsurface fluid distribution system.

The purpose of the program is to prevent the contamination of any underground sources of drinking water. Inventory information must be submitted for any existing Class V injection wells and before installation of new Class V injection wells. However, a permit is not required if it is determined that the well does not endanger underground sources of drinking water.

The program has two requirements:

  • Submitting basic inventory information about the stormwater drainage wells to the EPA; and
  • Constructing, operating, and closing the drainage well in a manner that does not endanger underground sources of drinking waters (USDWs).

  1. Enabling Legislation: Safe Drinking Water Act
  2. Required Permit Class V Injection Well Inventory
  3. Regulatory Authority: U.S. Environmental Protection Agency
  4. Applicability: Underground sources of drinking water
  5. Stormwater Relationship: Shallow stormwater disposal systems (for example, dry wells, sumps, drain tile, certain infiltration practices) placing stormwater below the land surface.

Mississippi National River and Recreation Area (MNRRA) Program

This is a joint federal, state, and local program, overseen by the National Park Service which provides coordination for 72 miles of the Mississippi River, four miles of the Minnesota River, and 54,000 acres of adjacent corridor lands. The MNRRA Comprehensive Management Plan adopts and incorporates by reference the state Critical Area Program, Shoreland Management Program, and other applicable state and regional land use management programs that implement the plan’s visions.

  1. Enabling Legislation: Minnesota Statutes, Section 116G; Minnesota Rules, Chapter 4410
  2. Required Permits: NA
  3. Regulatory Authority: National Park Service (oversight); DNR, Division of Waters; Local Government
  4. Applicability: Sections of the Mississippi and Minnesota River and designated corridor
  5. Stormwater Relationship: Activities within the national river and recreation area</p>

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 August 1, 2013 through July 31, 2018.
  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

Local level implementation

Many programs are administered at the local level. Some of those are discussed below.

Wetland Conservation Act

This program, begun in 1991, regulates drainage, fill, or excavation of wetlands in the state. Proposed projects are required to demonstrate through sequencing requirements that the project first seeks to avoid disturbing the wetland; second try to minimize any impact on the wetland; and finally, when impact is unavoidable, replaces any lost wetland acres, functions, and values. Certain wetland activities are exempt from the act, allowing projects with minimal impact or projects located on land where certain pre-established land uses are present to proceed without regulation

There are two categories for WCA permits:

  1. Water/Wetland Projects
  2. Water/Wetland Projects: Public Transportation and Linear Utility Projects

Projects disturbing wetlands may also require permits or approvals from the Department of Natural Resources, U.S Army Corps of Engineers, and Minnesota Pollution Control Agency. A joint application form has been developed that may be used for application to all of these agencies.

  1. Enabling Legislation: Minnesota Statutes 103G; Minnesota Rules Chapter 8420
  2. Required Permit: Water/Wetland Projects
  3. Regulatory Authority: Local Government Unit; Board of Water and Soil Resources (oversight)
  4. Applicability: Jurisdictional wetlands (meeting the criteria for soil, hydrology, and vegetation outlined in the 1987 Army Corps of Engineers Wetland Delineation Manual)
  5. Stormwater Relationship: Drainage, fill, or excavation of wetlands

Industrial Discharge

This program regulates and monitors industrial discharges into the Metropolitan Disposal System (public sanitary sewer system) to ensure compliance with local and federal regulations. Industrial users discharging wastewater into public sewers are required to apply for an industrial waste permit

There are three categories for industrial waste permits:

  1. Standard discharge permits
  2. Special discharge permits
  3. Liquid waste hauler permits

Below is a summary

  1. Enabling Legislation: Minnesota Statutes, Chapter 473
  2. Required Permit: Industrial Discharge Permit
  3. Regulatory Authority: Metropolitan Council; Minnesota Pollution Control Agency; Environmental Protection Agency
  4. Applicability: Metropolitan Disposal System (public sanitary sewers in Twin Cities Metropolitan area)
  5. Stormwater Relationship: Industrial discharges of wastewater or contaminated stormwater into public sanitary sewer system

Drainage

Public drainage administrative oversight is provided by designated Drainage Authorities. Drainage Authorities may be a County Board, a Joint Ditch Authority composed of representatives from multiple counties, a Watershed District or a Water Management Organization. Drainage law applies to public ditches and conveyance systems and consists of four elements; legal, engineering, environmental, and economic. The Drainage Authority has general authority for regulating and maintaining the public drainage system as it was designed. In accordance with M.S103E.411 Subp 2, the MPCA must approve any plan for connection or outlet of a municipal drainage system to a county drainage system.

  1. Enabling Legislation: Minnesota Statutes 103E; Minnesota Statutes 103D
  2. Required Permit: Local drainage permit
  3. Regulatory Authority: Drainage Authority
  4. Applicability: Public drainage system components
  5. Stormwater Relationship: Conveyance of stormwater

Shoreland Management Program

This program was created in 1969 in response to the Shoreland Management Act and applies to all land within a Shoreland District. Shoreland Districts are defined as lands within 1,000 feet of a lake which is greater than 25 acres (10 acres in municipalities) or within 300 feet of a river with a drainage area two square miles or greater and its designated floodplain defined from the ordinary high water level (OHWL)Local units of government are required to adopt the DNR minimum or stricter standards into their zoning ordinances and permit programs for the use and development of shoreland property. This includes a sanitary code, minimum lot size, minimum water frontage, building setbacks, building heights, land use, BMPs, shoreland alterations, subdivision, and PUD regulations

  1. Enabling Legislation: Minnesota Statutes, Section 103.F01-221; Minnesota Rules Chapter 6120
  2. Required Permit: Local government permits for building construction, installation of sewage treatment systems, and grading and filling
  3. Regulatory Authority: Local Government Unit; DNR, Division of Waters (oversight)
  4. Applicability: All lakes greater than 25 acres (10 acres in Municipalities) and rivers with a drainage area two square miles or greater and their associated floodplains
  5. Stormwater Relationship: Activities on all land within 1,000 feet of a designated lake and 300 feet of a designated river and its designated floodplain

Floodplain Management Program

This program was created in 1969 in response to the State Floodplain Management Act and regulates the construction of structures, roads, bridges or other facilities located within the 100-year floodplain areas

Local units of government for flood prone communities are required to adopt the DNR minimum standards, or stricter, for floodplain management into their ordinances and permit programs. They are also required to enroll and maintain eligibility in the DNR administered National Flood Insurance Program (NFIP), to protect new development and modifications to existing development from flood damages when locating in a flood prone area cannot be avoided.

  1. Enabling Legislation: Minnesota Statutes, Section 103.F01-165; Minnesota Rules Chapter 6120
  2. Required Permit: Local government permits for construction of structures, roads, bridges or other facilities within the floodplain
  3. Regulatory Authority: Local Government Unit; DNR, Division of Waters
  4. Applicability: All areas mapped within the 100-year floodplain
  5. Stormwater Relationship: Construction of structures, roads, bridges or other facilities on any lands within the 100-year floodplain

Lake Improvement District Program

Local citizen initiatives can petition counties to create lake improvement districts in order to address specific concerns within a lake watershed that cannot be addressed under normal governmental actions. Citizens and counties willing to undertake such initiatives gain greater local involvement in the management of their own lakes

  1. Enabling Legislation: Minnesota Statutes, Section 103B.501 - 103B.581; Minnesota Rules Chapter 6115
  2. Required Permit: Local government permits
  3. Regulatory Authority: Local Government Unit; DNR, Division of Waters
  4. Applicability: Lakes
  5. Stormwater Relationship: Activities affecting lakes and associated resources within a lake improvement district

Related information

The tables shown below include

  • a summary of federal and state programs; and
  • an aid to the user in determining which permits they may need for a specific project and which agencies to contact for more information.

The worksheet should not be viewed as a definitive list but rather as a resource to point the user in the right direction. The worksheet is provided as a means of organization and information gathering. Applicants should always check with their local zoning authority for more information on local requirements.

If a project is in, near, or draining to a Special Water then additional permit conditions designed to preserve and protect the quality and character of these unique waters will apply. Additional regulatory information that may be useful is located on various websites (see References) and includes the following:

  • a general list of agencies and contacts with a brief description of the agency, address, telephone, and Web site contact information;
  • a brief summary of the major federal and state enabling legislation that mandates or supports the above programs; and
  • links to model ordinances for a number of stormwater management activities.

Summary of federal and state stormwater related permits.
Link to this table

Permit Title Regulatory Agenc Enforcement Authority Implementation Authority Applicability Stormwater Regulated Activities
NPDES/SDS Construction Site Permit (Phase II) MPCA MPCA USEPA USEPA - Clean Water Act M.S. 115.01- 115.09 Mn. Rules 7090 Applies to all construction disturbing one or more acres of land, areas less than one acre if that activity is part of a “larger common plan of development or sale” that is greater than one acre, and MPCA designated construction activities disturbing less than one acre that have the potential for contribution to a violation of a water quality standard or for significant contribution of pollutants to water resources Stormwater discharge associated with road building, landscaping, clearing, grading, excavation, and construction of homes, office buildings, industrial parks, landfills and airports.
NPDES/SDS Municipal Separate Storm Sewer System Permit (Phase II) MPCA MPCA USEPA USEPA - Clean Water Act M.S. 115.01- 115.09 Mn. Rules 7001 and 7090 Applies to municipal separate storm sewer systems located in state and federal designated areas. On going site management and maintenance activities. Site management must include at a minimum the Six Minimum Control Measures: 1. public education and outreach, 2. public participation and involvement, 3. illicit discharge detection and elimination, 4. construction site storm water runoff control, 5. post construction storm water management, and 6. pollution prevention / good house keeping.
NPDES/SDS Industrial Site Permit (Phase II) MPCA MPCA USEPA USEPA - Clean Water Act M.S. 115.01- 115.09 Mn. Rules 7001 and 7090 Applies to public (municipal) and private operators of industrial facilities included in one of the 11 categories of industrial activity defined in the federal regulations by an industry’s Standard Industrial Classification (SIC) code or a narrative description of the activity found at the industrial site are required to apply for a permit On going site management and maintenance activities. Site management may include BMPs such as oil and grease separators, designated wash out locations, site sweeping, and storing materials indoors.
NPDES/SDS Feedlot Permit MPCA MPCA USEPA USEPA - Clean Water Act M.S.115.076 and 116.07 Mn. Rules 7001, 7020, 7050, and 7060 Applies to owners and operators of feedlots capable of holding 1,000 animal units or more or Concentrated Animal Feeding Operations (CAFOs) meeting criteria in 40 CFR § 122.23(b) (4). Stormwater discharge associated site location and expansion activities; construction activities; manure application, storage (stockpiling) location, and management; phosphorus management, pollutions prohibitions; and process wastewater and milk house wastes.
401 Water Quality Certification MPCA MPCA USEPA USEPA – Clean Water Act (33 U.S.C. 1341) M.S. 115.03 Mn. Rules 7001 Applies to all activities requiring a federal permit that may have discharge to state waters. Water quality impacts that may be generated from the structure, siting, or runoff management.
Section 404 Permit USACOE USACOE USEPA USEPA - Clean Water Act Section 404 (33 U.S.C. 1344) Applies to territorial seas; all navigable waters and adjacent wetlands; tributaries to navigable waters and adjacent wetlands; Interstate waters and adjacent wetlands; and all waters not identified above in which the destruction or degradation could affect interstate commerce Discharge of dredged or fill material into waters of the United States.
Section 10 Rivers and Harbors Act Permit USACOE USACOE Rivers and Harbors Act Section 10 Applies to all Navigable Waters of the U.S. Navigable Water designation is based on past, present or potential use for transportation or interstate commerce. Any work in, over or under a Navigable Water of the U.S or work that affects the course, location, condition or capacity of such waters.
Class V Injection Well Inventory and Permit USEPA USEPA Safe Drinking Water Act Applies to all potential underground sources of drinking water. Installation, operation, or abandonment of shallow disposal systems that are used to place stormwater below the land surface through a shaft or hole that is deeper than it is wide.
Public Waters Work Permit DNR DNR M.S. 103G.245 Mn. Rules 6115 Development activities below the ordinary high water level (OHWL) in public waters and public waters wetlands Filling, excavation, shore protection, bridges and culverts, structures, docks, marinas, water level controls, dredging, and dams.
Water Appropriations Permit DNR DNR 103G.255 Mn. Rules 6115.0600 Regulates surface and ground water appropriations and use of water Construction dewatering permits (erosion control and discharge conditions).
Calcareous Fen Management Plan DNR DNR MPCA 103G.223 Mn. Rules 8420.1010 Regulated drain, fill, otherwise alter or degrade calcareous fen Discharges that affect the quantity, quality, or chemistry of waters supporting the fen.
Utility Crossing License DNR DNR M.S. 84 Mn Rules 6135 Applies to utility crossing of any state land or public waters. Discharges or adverse effect to the water resource resulting from passage of any utility over, under, or across state land or public waters.
Water/Wetlands Project Permit (WCA) LGU (as designated in WCA)* DNR Wetland Conservation Act M.S. 103G Mn. Rules 8420 Applies to all jurisdictional wetlands. Draining, filling, and in some cases excavation, degradation of water quality due to untreated stormwater runoff.
Industrial Discharge Permit Met Council (Twin Cities Area Only) MPCA USEPA Mn. Rules 473 Applies to industrial users of the Metropolitan Disposal System (public sanitary sewers) Stormwater discharge, leachate, and groundwater where there is no prudent or feasible disposal alternatives.
Drainage Permit or Permission Drainage Authority Drainage Authority LGU* M.S. 103D M.S. 103E Applies to the public drainage system. Introduction of stormwater into the system, conveyance of stormwater through the system, and discharge of stormwater from the system.
Other Local Permits LGUs* LGU* DNR MPCA Various Applies to any additional local regulations which may include resources in the above categories, shoreland management, floodplain management, lake improvement districts, landfills, wastewater, sand and gravel operations, hot mixing, dewatering, TMDLs, etc. Various.
*C.F.R. - Code of Federal Regulations
  • M.S. - Minnesota Statute
  • U.S.C. - United States Code
  • LGU = local governmental unit (Counties, Soil and Water Conservation Districts, Water Management Organizations, Watershed Districts, Metropolitan Council, Lake Associations, Municipalities, Townships, Villages, etc.)


Permitting worksheet.
Link to this table

Step 1: Determine if your project entails a regulated activity:
Is the project: Yes No Not sure? Primary Agency to Contact Related Permits You May Need
disturbing > 1 acre? Check project plans MPCA, MS4 NPDES/SDS Construction Permit
dewatering? Check project plans DNR Water Appropriations Permit
appropriating water? Check project plans DNR Water Appropriations Permit
an industrial discharge? Check project plans MPCA Met Council NPDES/SDS Industrial Permit Industrial Waste Disposal Permit
a feedlot operation? Check project plans MPCA MDA NPDES/SDS Feedlot Permit
discharging to Special Waters? Check Special Waters list MPCA NPDES/SDS Permits
discharging to surface waters? Check project plans MPCA DNR NPDES/SDS Permit Water Appropriations Permit
disposing/injecting stormwater into the shallow subsurface? Check project plans USEPA Class V Injection Well Inventory Class V Injection Well Permit
draining wetland? Check NWI Check wetland delineation USACE DNR MPCA BWSR, LGU Section 404 Permit Public Waters Permit Section 401 Water Quality Certification Waters/Wetlands (WCA) Permit
filling wetland? Check NWI Check wetland delineation USACE DNR MPCA WSR, LGU Section 404 Permit Public Waters Permit Section 401 Water Quality Certification Waters/Wetlands (WCA) Permit
excavating wetland? Check NWI Check wetland delineation USACE DNR MPCA WSR, LGU Section 404 Permit Public Waters Permit Section 401 Water Quality Certification Waters/Wetlands (WCA) Permit
innundating wetland? Check NWI Check wetland delineation USACE DNR MPCA WSR, LGU Section 404 Permit Public Waters Permit Section 401 Water Quality Certification Waters/Wetlands (WCA) Permit
affecting a calcareous fen? Check calcareous fens list X X
working below the ordinary high water level or in a Public Water? Check OHWL Check PWI DNR Public Waters Permit
a utility crossing (e.g. pipe, transmission line, etc.)? Check project plans DNR, public owner of land Utility Crossing License, State/Public Landowner Permission
Step 2: Determine the receiving water
Is the project area is in, near, or draining directly to: Yes No Not Sure? Primary Agency to Contact Considerations and Related Permits You May Need
a trout lake or lake trout lake? Check trout lakes DNR Special Permit Conditions Apply
DNR public waters? Check PWI DNR Public Waters permit
a water of the US? Check Waters of US USACE Section 404 or Section 10 Permit and Section 401 Water Quality Certification
a trout stream? Check trout streams DNR Special Permit Conditions Apply
a wild, scenic, or recreational river? Check WSR Rivers DNR Special Permit Conditions Apply
the Upper Mississippi River? Check Special Waters DNR Special Permit Conditions Apply
a public drainage ditch? Contact Drainage Authority Drainage Authority Drainage permit/permission
wetland? Check NWI Check wetland delineation BWSR, LGU WCA Permit, Section 404 Permit, Public Waters Permit, and/or Section 401 Water Quality Certification
DNR public waters wetlands? Check PWI DNR WCA Permit, Section 404 Permit, Public Waters Permit, and/or Section 401 Water Quality Certification
a calcareous fen? Check Calcareous Fens list DNR, MPCA Approved calcareous fen management plan and individual NPDES/SDS permit
an impaired water or TMDL listed water? Check 303d list MPCA Special Permit Conditions Apply
outstanding resource value waters (ORVWs)? Check ORVWs MPCA Special Permit Conditions Apply
Step 3: Determine if your project area is in, near, or draining to special areas:
Is the project area in, near, or draining directly to: Yes No Not Sure? Primary Agency to Contact Considerations and Related Permits You May Need
MS4? Check with MS4 (City, Watershed, Mn/DOT) MPCA, LGU NPDES/SDS MS4 Permit
a construction site? Check with LGU MPCA, LGU NPDES/SDS Construction Permit
an industrial site? Check with LGU MPCA Met Council NPDES/SDS Industrial Permit or Industrial Waste Disposal Permit
a feedlot operation? Check with LGU MPCA NPDES/SDS Feedlot Permit
a coastal zone (Lake Superior)? Check Coastal Zone DNR Special Permit Conditions Apply
the Mississippi River Critical Area (MRCA)? Check MRCA DNR Special Permit Conditions Apply
a shoreland district? Check with LGU LGU Special Permit Conditions Apply
a floodplain, floodway, or flood zone? Check FEMA maps LGU Special Permit Conditions Apply
a wilderness area? Check Wilderness Areas NPS, USFS, BLM, USFWS Special Permit Conditions Apply
a scientific or natural area? Check SNAs DNR Special Permit Conditions Apply
a lake improvement district? Check with LGU LGU Special Permit Conditions Apply
a dewatering site? Check project plans DNR Water Appropriations Permit
a watershed district or water management organization? Check WD/WMOs WD/WMO,BWSR Watershed Permits
an Indian Reservation? Check Reservations Tribal government Tribal Permits
federally protected land? Check with LGU NPS, USFS, BLM, USFWS Special Permit Conditions Apply
a source water protection area? Check with LGU LGU, MDH Special Permit Conditions Apply
a drinking water protection area? Check with LGU LGU, MDH Special Permit Conditions Apply
a karst area? Check Karst DNR, LGU Special Permit Conditions Apply
a wellhead protection area? Check with LGU LGU, MDH Special Permit Conditions Apply
Step 4: Compile a list of agencies to consult and permits you may need (from lines marked “yes” above):
Agency to consult: Permits which may be required:
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Step 5: Consult your local zoning authority and watershed organization for more information on local regulations/requirements/permits
Local Zoning Authority: Local Watershed Organization:
Contact Name: Contact Name:
Address: Address:
City, State, Zip: City, State, Zip:
Telephone: Telephone:
Email: Email:
Web: Web:


References

This page was last modified on 10 February 2016, at 14:31.

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