Waterways Permitting Process

DNR Jurisdiction Over Waterways

The DNR regulates activities that may impact navigable waters below the Ordinary High Water Mark. A navigable waterway is defined through case law as any waterway that has a defined bed and bank, and upon which it is possible to float a canoe or small watercraft on a recurring basis. The Ordinary High Water Mark is defined as the point on the bank or shore up to which the presence and action of the water is so continuous as to leave a distinct mark either by erosion, destruction of terrestrial vegetation or other easily recognized characteristic.

Three-Tier Permitting System

The DNR implements a three-tier system of project authorization based on the expected level of environmental impact: exemptions, general permits and individual permits. If your project may impact a navigable waterway, it may be exempt if it meets eligibility criteria in one of the exemption checklists below. If it is not exempt, it may qualify for a General Permit if it meets the eligibility criteria in one of the General Permit checklists below. If it is not eligible for a General Permit, you must apply for an Individual Permit.

Other Permitting May be Required

To determine if a local permit or a federal permit is required for your project, contact your city or county zoning authority and the U.S. Army Corps of Engineers – St. Paul District Office.

For some waterway projects, a water quality certification (WQC) may be required from DNR as the certifying authority under the Clean Water Act Section 401. WQC requests will be considered complete through a waterway permit application and the DNR Waterways Program typically reviews WQC requests in parallel with permit review. See WQC Request Completeness Elements for the full list of requirements. 

State law requires a landowner with a project site that is 1 acre or larger in size to obtain a construction site stormwater permit. To submit a notice of intent, visit the DNR Stormwater Runoff Permitting page.

Start an Application

Please visit the DNR Water ePermitting System to start an application. Note that you will need a WAMS ID. Select the "Waterway and Wetland” tab on the left side of the page and choose your general permit or individual permit activity.

Fees: All waterway permit applications require a fee under state law. See "Waterway Permit Fees" in our permit fee sheet.

Waterway Exemptions

Chapter 30, Wis. Stats. provides permit exemptions for the following activities in navigable waters. By law, most exemptions are not allowed in Areas of Special Natural Resource Interest (ASNRI). These areas include state natural areas, trout streams, outstanding or exceptional resource waters and other waters designated by the DNR as having significant scientific value.

Note that projects that are exempt from DNR waterway permitting may still require floodplain, shoreland, and other approvals from your local zoning office.

1. Determine Location. To determine if your project site is an ASNRI or public rights feature (PRF), visit the Surface Water Data Viewer, find the waterway where your project is being planned, and use the designated waters data layer. See Property Lookup for Designated Waters for instructions on how to use this mapping tool.
2. Project Design. To determine your project needs and design, you may wish to consult professionals and contractors for ideas.
3. Exemption Eligibility. Review the exemption checklist for your project type below to determine if your project qualifies for an exemption.
4. Implementation. If you determine that your project is exempt from permit requirements, and you have all other necessary DNR/state, local, and federal permits, you can implement the project.

Waterway Exempt Project Checklists:

Culvert

• Culvert replacement (same location)

Dredging

• Manual dredging

Fish and Wildlife Habitat Structures

• Fish crib
• Half-log structure
• Spawning reef
• Tree drop
• Wildlife habitat structure
• Wing deflector

Miscellaneous Structures

• Dry fire hydrant
• Intake or outfall structure
• Pilings

Recreational Structures

• Seasonal boat shelter, boat lift and boat hoist
• Pier, dock or wharf
• Shoreline maintenance
• Swimming raft

Shoreline Erosion Control Structures

• Biological shore erosion control
• Riprap​​​

Waterway General Permits

A variety of waterways projects have a general permit option available if your project meets specific size, design and technical requirements. The general permit process generally takes 30 days after the application has been submitted.

General Permit Process

1. Review the appropriate General Permit Checklist below to determine if your project meets all the requirements.
2. Use the DNR Water ePermitting System to begin and complete a General Permit application.
3. The DNR has 30 days to review the application for completeness and notify the applicant. The DNR can request additional information one time within these 30 days, which would pause the 30-day period until all information requested is received.
4. After the 30-days total review time, the DNR will communicate a permit decision to you.

General Permit Process Timeline

Waterway General Permits and Checklists:

Agricultural Water Quality Improvement Activities

• Waterway and Wetland General Permit 18 - Agricultural Water Quality Improvement Projects
  • GP18 Application Checklist - Ag Water Quality Projects

Bridges, Culverts, and Fords

• Waterway General Permit 21 - Crossings: Culvert, Clear-Span Bridges, and Fords
  • GP 21 Application Checklist - Crossings (3500-130)
• Waterway General Permit 12 - Temporary Crossings for Forest Management Activities
  • GP12 Application Checklist - Temporary Waterway Crossing (3500-131)

Dredging and Grading

• Grading General Permit Standards for Grading - see NR 341.08, Wis. Adm. Code., for eligibility criteria.
  • GP Application Checklist - Grading (3500-146)
• Waterway General Permit 13 - Dredging Maintenance of a Previously Dredged Area
  • GP 13 Application Checklist - Previously Dredged Area (3500-132)
• Waterway General Permit 5 - Dredging To Remove Accumulated Plant and Animal Nuisance Deposits
  • GP 5 Application Checklist - Dredging Nuisance Deposits
• Waterway General Permit 17 - Small Scale Dredging
  • GP 17 Application Checklist - Small Scale Dredging
• Waterway General Permit 20 - Dredging for Riparian Navigation on Impoundments
  • GP 20 Application Checklist - Riparian Navigation Dredging
• General Permit Standards for other Dredging Purposes - see NR 345.04, Wis. Admin. Code.
  • General Permit Application Checklists:
    • Dredging - Invasive or Non-Native Species Management
    • Dredging - Installation of Utility Crossing(s)
    • Dredging - Jetting Aquatic Plants (3500-154)
    • Dredging - Maintenance within a Drainage District
    • Dredging - Stream (Less than 25 Yards)

Fish and Wildlife Habitat Structures

• Waterway General Permit 6 - Fish and Wildlife Habitat Structures
  • GP 6 Application Checklist - Habitat Structures
• Waterway General Permit 14 - Stream Habitat Projects Implemented by the U.S. Forest Service
• Waterway General Permit 15 - Stream Habitat Projects Designed by Govt. Agencies
  • General Permit Application Checklist - Stream Habitat Govt. Agencies (3500-174)

Miscellaneous Structures

• General Permit Standards - see NR 329.04 (2), Wis. Admin. Code.
  • General Permit Application Checklists:
    • Dry Fire Hydrant (3500-153)
    • Intake or Outfall Structure (3500-145)
    • Pilings (3500-157)

Ponds

• Waterway General Permit 23 - Ponds 
  • GP 23 Application Checklist Ponds 

Recreational Structures

• Waterway General Permit 19 - Permanent Boat Shelters
  • GP 19 Application Checklist Permanent Boat Shelters
• General Permit Standards for other Activities - see NR 329.04 (2), Wis. Admin. Code.
  • General Permit Application Checklists:
    • Boat Ramp (3500-172)
    • Pea Gravel Blanket (3500-149)
    • Weed Rake (3500-143)

Shoreline Erosion Control Structures

• General Permit Standards - See NR 328.05 and NR 328.35
  • General Permit Application Checklists:
    • Lake Shore Erosion Control - Biological
    • Lake Shore Erosion Control - Riprap
    • Lake Shore Erosion Control - Riprap Repair (3500-161)
    • Lake Shore Erosion Control - Riprap Replacement (3500-173)
    • Lake Shore Erosion Control - Seawall Replacement
    • Lake Shore Erosion Control - Seawall Replacement with Riprap (3500-150)
    • Stream Bank Erosion Control - Biostabilization (3500-152)
    • Stream Bank Erosion Control - Integrated Bank Protection
    • Stream Bank Erosion Control - Repair of Riprap (Placed Prior to August 1, 2007)
    • Stream Bank Erosion Control - Replacement of Structure with Biostabilization
    • Stream Bank Erosion Control - Replacement of Structure with Integrated Bank Treatment

Utility Projects

• Wetland and Waterway General Permit 3 - Utility Projects
• Wetland and Waterway GP3 Application Checklist

Waterway Individual Permits

For a waterway project that does not offer an exemption or general permit option, or that does not meet the requirements of those options, you may submit an individual permit application to the DNR. The individual permit process takes longer and involves a public comment period and potentially a public hearing. The review process typically takes 105-135 days to complete.

Individual Permit Process

1. Use the DNR Water ePermitting System to begin and complete an Individual Permit application.
2. The DNR has 30 days to review the application for completeness and notify the applicant. The DNR can request additional information one time within these 30 days, which would pause the 30-day period until all information requested is received.
3. The DNR has 45 days to provide a public comment period.
4. If requested by the public or by the DNR, the DNR has 30 days to provide a public hearing.
5. The DNR has 30 days from the end of the public comment period to communicate a decision to you about the permit application.

Individual Permit Process Timeline