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. 

This is a partial list of typically regulated activities:

• Boathouse repair and maintenance.
• Construction of ponds within 500 ft. of a navigable waterway
• Dredging, meaning removal of material from the bed of a lake or stream.
• Grading on the bank of a navigable waterway.
• Placing structures, such as piers, boat shelters, riprap, seawalls, fish habitat structures, pilings, intake/outfall pipes, etc. 
• Placing crossings, including bridges, culverts, and fords.

What Are My Waterway Permitting Options?

Waterway Exemptions

Projects impacting wetlands that meet all of the criteria for one of the following exemptions do not need a DNR wetland permit. By law, most exemptions are not allowed in Areas of Special Natural Resource Interest (ASNRI). These designated 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.

How do I determine if my stream, river, or lake is not an ASNRI and eligible for one of the exemptions below?

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.

Do I need to apply if my project is exempt from needing a DNR waterway permit?

If your project meets all of the exemption criteria in one of the checklists below, you do not need to contact DNR prior to construction. If you prefer that DNR Waterways reviews the project, you may submit a voluntary exemption review request to the local Water Management Specialist by email and include the following information:

• A statement that describes the proposed activity.
• The site location.
• The construction timing and methods that will be used.
• The project scope and design.
• A demonstration that the proposed activity will not cause a material injury to the riparian rights of any riparian owners.
• If the exemption request is from the project proponent, a statement of consent to allow the department to inspect the site.

DNR Waterways will then provide a response within 15 working days under the process outlined in s. NR 300.04 (6), Wis. Adm. Code. There is no fee to submit a voluntary exemption review request.

Culvert Replacement Exemption

• Culvert replacement (same location)

Dredging Exemption

• Manual dredging

Fish and Wildlife Habitat Structures Exemptions

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

Miscellaneous Structures Exemptions

• Dry fire hydrant
• Intake or outfall structure
• Pilings

Recreational Structures Exemptions

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

Shoreline Erosion Control Structures Exemptions

• Biological shore erosion control
• Riprap

Other Permits May Be Required

USACE Wetland Permit: To determine if a federal permit is required for your project, contact the U.S. Army Corps of Engineers – St. Paul District Office. Permit applications submitted to the DNR are reviewed by a USACE St. Paul District project manager. A USACE checklist will be required with the application as a screening tool. The federal wetland permitting process is a separate process.

Water Quality Certification: 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 wetland 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.

Stormwater Notice of Intent (NOI): State law requires a landowner with a project site that is 1 acre or larger to obtain a construction site stormwater permit. Visit the DNR Stormwater Runoff Permitting page to submit a notice of intent.

Floodplain and Shoreland Zoning Authorization: If your project is in a regulatory floodplain or in a shoreland-wetland, local or county zoning regulations may apply. Please contact your city or county zoning authority.

Waterway General Permits

A variety of waterways projects have a general permit option available if your project meets specific size, design and technical requirements. Review the appropriate activity general permit checklist below, and if your project meets all of the eligibility criteria, you may apply through the DNR Water ePermitting system. The general permit review process generally takes 30 days after the application has been submitted.

How do I apply for a waterways general permit?

1. The applicant uses the DNR Water ePermitting System to submit a general permit application.
   • Select "Waterway and Wetlands" from the menu on the left side.
   • Select "Start General Permit".
   • Select the appropriate general permit type for your project.
   • Provide all required information and attachments and pay the appropriate permit fee.
2. The DNR notifies the applicant if any items are missing that must be submitted.
3. After 30 days, the DNR grants the permit if the application meets all eligibility criteria in the general permit checklist and avoids and minimizes wetlands to the greatest extent practicable.
4. The DNR may require the applicant to apply for an individual permit if the general permit conditions are insufficient to ensure that the project will cause only minimal adverse environmental impacts.

What is required in a statewide general permit application?

The following items are standard requirements for any wetland general permit application:

• Proof of land ownership.
• Project plans and specs that show the project in relation to the ordinary high water mark and the owner's riparian zone, all proposed roads, structures, excavation, etc., and areas of the stream, river, or lake to be impacted.
• Top, side, and cross section plan profiles.
• Detailed narrative including erosion control measures and proposed location for dredged or excavated materials. 
• Construction schedule and sequence.
• Project site maps including soils, wetlands, topography, floodplain, and aerial photos.
• Current photographs of the project areas.

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

• 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)

Grading

• Grading General Permit Standards for Grading - see NR 341.08, Wis. Adm. Code., for eligibility criteria.
  • GP Application Checklist - Grading (3500-146)

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 (applicant must be a utility entity)
• 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