Are Lily Pads Protected in Wisconsin?
As of September 2026: This page summarizes Wis. Admin. Code NR 109 and published DNR guidance on native aquatic plants. Confirm anything specific to your lake with your regional APM coordinator.
Yes. The two lily pad plants you'll find on a Wisconsin lake, white water lily and spatterdock, are both native aquatic plants, and native plants are protected under the same rule that covers coontail, native watermilfoil, and every other rooted plant that isn't on the state's invasive list. Protected doesn't mean untouchable. It means removal is regulated instead of unrestricted, and a homeowner working near a pier usually has a legal path that needs no permit at all.
What plant are you actually looking at?
"Lily pad" usually means one of two native species in Wisconsin waters.
- White water lily (Nymphaea odorata). Round, notched floating leaves, fragrant white flowers with many narrow petals, blooming through summer.
- Spatterdock, or yellow pond lily (Nuphar variegata). Larger, heart-shaped leaves that often stand partly above the water, with a rounded yellow flower that looks more like a cup than a lily.
Both root from thick rhizomes buried in the lake bottom, which is the detail that matters most for removal. Clipping the visible leaf does very little; the plant regrows from the root within the same season.
Why native status changes the removal rule
Wisconsin's aquatic plant management rules, chapter NR 109 of the Wisconsin Administrative Code, draw a hard line between native and invasive vegetation. Invasive species like Eurasian watermilfoil get an easier removal path because the state wants them gone. Native species, lily pads included, get the opposite treatment: the DNR wants them to stay in place at a lake-wide level, even when one homeowner finds them inconvenient at a swim area or a boat lane. That's the same logic that protects coontail and native pondweeds, not something specific to lilies.
When you can remove lily pads without a permit
Under NR 109.06(2)(a)1., a shoreline owner can hand-remove native aquatic plants, lily pads among them, in a single corridor no wider than 30 feet measured along the shore, with no permit, as long as the pier, boatlift, and swim raft all sit inside that same 30-foot zone. Allowed tools are hand-pulling, a string trimmer, or a push mower on exposed lakebed. The practical problem with lily pads specifically is the rhizome: hand-pulling a mature plant means reaching into the muck for the root mass, not just skimming the leaves, and you have to get the cut material out of the water and onto land afterward.
If your lake is 10 acres or smaller and entirely on your own property, the separate small-waterbody exemption under NR 109.06(1) may cover manual or mechanical removal lake-wide, not just in a 30-foot strip. That exemption is about the whole waterbody's size and ownership, not the plant.
When you need a permit
Removing lily pads from an area wider than the 30-foot corridor, using a mechanical cutter or harvester, or applying an herbicide to control them all require DNR sign-off first. A wider lily pad bed usually means the neighboring bottom is soft muck, which is also where mechanical equipment and bottom barriers get regulated more closely. If wild rice or a listed species grows nearby, even the 30-foot exemption can be off the table, so a lake with a sensitive-area designation needs a call to the regional APM coordinator before anything gets pulled.
Full permit mechanics, including the NR 107 vs. NR 109 split and the online application process, are on the DNR permit rules page.
Lily pads next to other plants
A lily pad bed rarely grows alone. It's common to find coontail or native watermilfoil rooted in the same soft bottom, and Eurasian watermilfoil sometimes moves into the same cove. Before you decide how much of a bed to clear, confirm what's actually growing there; see why the DNR treats native and invasive plants differently and the step-by-step exemption rules on manual removal without a permit.