Juneau County, Wisconsin Building Permit Guide

In Juneau County the county and the local municipality split the work. Sanitation & Zoning, at 650 Prairie Street in Mauston (608-847-9391), issues septic (sanitary) permits for private onsite systems and zoning permits on shoreland and floodplain land, while the town, village or city issues the building permit under the Uniform Dwelling Code. The county’s own checklist puts the sanitary permit first, and its March 1, 2026 fee sheet doubles every fee for work started without a permit.

What work requires permits in Juneau County?

The county’s permits follow water and wastewater rather than buildings in general. A county zoning permit is needed before any construction starts on land within 1,000 feet of a lake or flowage, within 300 feet of a navigable river or stream, or in a floodplain. A county sanitary permit is needed when a private onsite system is installed, changed or newly connected. Away from water, the building and land use permits come from the town, village or city.

The county’s permit application states plainly that township permits are also required, so a lakeside house needs both the county zoning permit and the local building permit. A county permit is void if construction has not started within one year of issue.

What the county decides and what the state holds

Juneau County writes the local rules on shorelands, floodplains, private sewage (Chapter 15, Private Onsite Wastewater Treatment Systems) and land division (Chapter 23). Its general shoreland provisions set a 75-foot setback from the ordinary high-water mark, side yards of at least 10 feet with 25 feet combined, and limits on clearing in the 35-foot strip along the shore, where no more than 30 feet in any 100 feet may be clear cut. Road setbacks in the shoreland area run from 140 feet from the centerline of a state or federal highway (or 70 feet from the right of way) down to 63 feet from the centerline of a subdivision street.

The construction standards themselves are the state’s. Juneau County holds no Uniform Dwelling Code delegation of its own, so the plan review and inspection of a new one- or two-family home belong to the local municipality, and commercial buildings follow the state plan approval process before a local permit.

Juneau County building department: who handles permitting

Sanitation & Zoning, headed by Administrator David Gruen, works under the Land, Forestry, Parks & Zoning Committee. It runs the sanitary program, shoreland and floodplain zoning, land use permits, certified survey map review with the County Surveyor, and non-metallic mining reclamation. Because staff work in the field, the department notes that its office hours can vary.

Towns, villages and cities: who permits a new home

The state’s list of Uniform Dwelling Code delegations, current as of September 24, 2026, shows a delegation for every city and village in Juneau County and for 18 of its 19 towns. Each of those municipalities issues the permit for a new one- or two-family dwelling and arranges its inspections; where the list names an inspection agency, it shows General Engineering for the City of Elroy, the Town of Germantown and the Village of Necedah. Populations are Census estimates.

Juneau County permit types and application documents

One county form, the Juneau County Permit Application, covers land use permits, special exceptions and building permits in the shoreland and floodplain areas. It asks for the parcel number and legal description, lot size, the type of work (new building, addition, moving, alteration, filling, dredging, grading or shoreline rip-rap), the use, the zoning district, the building size, height, stories and bedrooms, and the sanitary permit number. A building site map drawn to scale must show the lot, every existing and proposed building and its distances, the well, the septic tank and the absorption field, and north.

Residential permits

For a rural house the county’s Rural Building Beginning Procedures sheet sets the order. A certified soil tester bores the lot and files a soil report; a licensed plumber designs the system from that report and applies for the sanitary permit on state form SBD-6398; once county and state approvals are in, the sanitary permit issues. With a copy of it and a plot plan, the owner applies for the land use or building permit to the town or, where the county ordinances apply, to Sanitation & Zoning. Shoreland and floodplain sites also need the county building permit.

Building or remodeling a home here? Alliance handles home building permits, so the crew isn't waiting on the counter.

Commercial permits

Commercial buildings near water or in a floodplain use the same county application, and commercial septic systems carry a separate plan review fee: $250 for a conventional system under 1,000 gallons a day. Building plan approval comes from the state or a delegated municipality, and the local building permit comes from the town, village or city.

For tenant improvements and new commercial builds, Alliance handles commercial permit filing through issuance. More on this: commercial building permits explained.

What comes before the building permit

• Soil test and sanitary permit. First in the county’s sequence for any lot without public sewer.
• Survey map. A new lot of 15 acres or less is created by certified survey map, reviewed by the County Surveyor, Sanitation & Zoning and the County Clerk, with at least 40 feet of road frontage; some towns require more.
• Shoreland or floodplain permit. Before any construction within the shoreland distances or in a floodplain; the department posts guidelines for residential development in a floodplain.
• State and federal water permits. The county form asks for Army Corps of Engineers or DNR permits where the project needs them.
• Special exception or variance. Heard at a public hearing for $1,000 plus the legal notice costs.

Juneau County zoning, sanitary and building-permit costs

The county’s fee sheet, dated March 1, 2026, covers sanitary, shoreland, floodplain, hearing and land division fees. Building permit fees for a house are set by the town, village or city that issues the permit and are not on the county sheet.

Soil saturation determinations cost $100 by the hydrograph method, $150 by controlled flowage and $200 with groundwater monitoring wells. The Wisconsin Fund grant application fee is $200, although the county reports no grant funding available at this time.

For a lakeside house on a private system, the county charges add up to $750 at a minimum: a $550 sanitary permit and a $200 shoreland building permit, with the soil test, the plumber and the local building permit paid separately.

Trade permits and who may pull them

Juneau County ties its septic work to licensed trades. Its sanitary permit application and its reconnect application must both be completed by a licensed plumber, and the soil evaluation that comes first must be done by a certified soil tester; the department posts lists of certified soil testers and plumbers and of septic tank pumpers.

• Electrical, plumbing and HVAC in a new house. Inspected as part of the dwelling permit by the town, village or city’s UDC inspector, not by the county.
• Septic. Sanitary permits, reconnections and system repairs go through Sanitation & Zoning on plumber-filed applications; a change of plumber on an open permit is $75.
• Maintenance. Existing systems fall under the county’s private sewage septic system maintenance program, and pumping is done by the pumpers on the county’s list.
• Builders. A contractor building a one- or two-family home needs the state Dwelling Contractor certification and a certified Dwelling Contractor Qualifier before a local permit can issue; an owner-occupant building a home for themselves is exempt.

How to apply for a Juneau County permit

Review, corrections and what causes delay

The sanitary permit sets the pace: it waits on the soil report, the plumber’s design and both county and state approvals, and the land use or building permit needs a copy of it. Some sites also need a soil saturation determination. Applications without a site map showing distances to the water, lot lines, well and septic are not complete. Variances and special exceptions need a public hearing and published notice. The county offers an expedited permit and review for $250 at its discretion.

Inspections and final approval in Juneau County

The county inspects septic installations; a same-day inspection costs $250. The construction inspections for a new house, from footings through the final, are the local UDC inspector’s, and any occupancy permit for the house comes from that same local office.

Once a system is in use it falls under the county’s septic maintenance program. On shorelands the county also enforces the cutting limits in the 35-foot strip and asks owners to call the zoning administrator before any filling, grading, dredging or excavating, which may or may not be allowed.

Starting any work without the needed permit, whether septic, shoreland or floodplain, doubles every fee on the county sheet.

Wisconsin building code

FEMA’s Community Status Book lists Juneau County (community 550580) as participating in the National Flood Insurance Program, with a current effective flood map dated October 16, 2012.

Wisconsin's Uniform Dwelling Code covers one- and two-family homes. Its Commercial Building Code covers public buildings, workplaces and buildings of three or more units. Local ordinances must conform to both. Wisconsin rules

Juneau County permit search and official resources

To ask about an existing sanitary or zoning permit on a parcel, call Sanitation & Zoning at 608-847-9391 with the parcel number; the county’s GIS maps show parcels and the department posts floodplain and wetland maps. For a house’s building permit record, ask the town, village or city that issued the permit.

• Juneau County Sanitation & Zoning
• Sanitary permits and septic information
• Shoreland zoning and permit application
• Floodplain zoning
• Survey map review
• Juneau County fees (March 1, 2026)
• Rural Building Beginning Procedures
• Juneau County permit application
• General shoreland zoning provisions
• Land and Water Resources: manure storage permit
• Juneau County Code of Ordinances
• DSPS list of UDC delegated agents
• DSPS Inspector Lookup Tool
• FEMA Community Status Book, Wisconsin

Juneau County building permit FAQ

Does Juneau County issue building permits for houses?

Not under the Uniform Dwelling Code. The county issues sanitary, shoreland, floodplain and land use permits; the dwelling permit comes from the town, village or city.

Which comes first, the septic or the building permit?

The sanitary permit. The county’s procedure sheet requires a copy of it with the land use or building application.

How much is a septic permit in Juneau County?

$550 for a conventional, mound, at-grade, in-ground pressure, system-in-fill or holding tank system, under the March 1, 2026 fee sheet.

Do I need a county permit to build near a lake?

Yes, within 1,000 feet of a lake or flowage, 300 feet of a navigable river or stream, or in a floodplain: $200 for a house and $100 for an accessory building.

How far from the water must I build?

At least 75 feet from the ordinary high-water mark, with limited exceptions for stairs, walkways and piers.

Who inspects a new house in the Town of Wonewoc?

The town is not on the state’s delegation list, so a DSPS-appointed UDC inspector does; the state’s Inspector Lookup Tool finds them.

What if I start without a permit?

All county permit fees are doubled for after-the-fact applications.

Does adding a bedroom need a sanitary permit?

Yes. Adding bedrooms, or an addition of 25% or more of the existing area, is one of the county’s sanitary permit triggers.

Simplify Juneau County permitting with Alliance Permitting

Alliance Permitting is a permit documentation and submission company in Wisconsin. We prepare your paperwork, file it correctly and coordinate with the permitting authority through issuance. We are not a contractor and we do not perform licensed plan review or inspections; that work stays with your licensed team and the jurisdiction.

This guide is provided by Alliance Permitting for general information about Juneau County permitting. Requirements, fees, and procedures change; confirm details with the permitting authority before relying on them.