Reader support helps keep the reviews honest and the site humming. As an Amazon Associate, I earn from qualifying purchases.7 Best Herbicide For Water Lilies | Pond-Safe Lily Killer

Check Price on Amazon

Kills the whole water lily from root to leaf, and works on over 185 other weed types — so you do not need a separate product for shoreline brush.

This is the herbicide to reach for when you want one product that handles water lilies, emergent brush (plants growing at the water’s edge), and shoreline weeds without needing three different bottles. It contains 27.8% Imazapyr, a systemic active ingredient that moves through the plant and kills the roots, unlike a contact spray that just burns the leaves. The manufacturer says it provides long-lasting residual control, meaning a single treatment can keep your pond clear for the whole growing season.

It gives you several application options — cut stump, basal bark (treating the base of the stem), stem injection, and spot treatment — so you can be precise around desirable plants. The liquid volume is 1 quart (32 fluid ounces), making it a concentrated option that mixes before spraying. One downside is that its broad-spectrum power means it will kill any vegetation it touches, so you need to be careful with overspray near trees or ornamentals you want to keep.

Unlike the Atticus Semera SC which is a faster-acting contact herbicide with 44% flumioxazin at 8 fluid ounces, the Alligare Ecomazapyr is a slow systemic that delivers full root-kill over time. The trade-off is patience — you may not see the lily pads die back for a week or two, but buyers report that when they go, they stay gone.

Check Price on Amazon

Burns back floating weeds in a few days, and stops new seeds from sprouting for up to six months — so you get fast visible results plus lasting prevention.

This liquid concentrate uses 44% flumioxazin, which is a fast-acting contact herbicide that also has residual pre-emerge power (pre-emerge means it stops weed seeds from sprouting). That means it kills the water lilies and floating weeds you see now, while also stopping new seeds from germinating for up to six months. Atticus says one application works all season, and because it offers both pre-emerge and post-emerge control (post-emerge means it kills weeds that have already grown) up to 2 inches in height, you have some timing forgiveness if you missed the early window.

At only 8 fluid ounces total, this is a compact product ideal for spot treatments around a dock or small pond. It is noticeably smaller than the Alligare Ecomazapyr which is 32 ounces — at 8 fluid ounces versus the Alligare Ecomazapyr at 32 fluid ounces — so you will need to buy more if you have a larger infestation. It controls a good list of aquatic weeds including duckweed, alligator weed, coontail, hydrilla, pondweed, water fern, water lettuce, and watermilfoil, though water lilies are not explicitly listed in the coverage label, so confirm your specific weed on the label.

Owners mention that the liquid mixes easily in a standard tank sprayer and shows visible results within a couple of days on floating weeds. The catch is that it is primarily a contact killer, so while it burns back lily leaves fast, it may not fully kill the rhizome (the thick underwater stem) on its own — heavy water lily growth may require a follow-up systemic.

Check Price on Amazon

Gives you the most active ingredient per container at 51% flumioxazin — so you use less product for each application than you would with the 44% liquid version.

This is the concentrated granular version of flumioxazin, and at 51% active ingredient (compared to 44% in the SC liquid), it is slightly more potent per ounce. It comes as a water-dispersible granule (WDG — a dry powder that dissolves in water for spray application), meaning you mix it with water in a sprayer, and it goes to work as a fast-acting contact herbicide with pre-emerge residual (killing existing weeds and stopping new seeds). The manufacturer says it offers six-month weed control with one spray, and it handles submerged, emergent, and floating weeds including duckweed, alligator weed, coontail, hydrilla, pondweed. Water lilies are not explicitly listed but it targets the same floating weed family.

At 16 ounces (1 pound), the total weight is comparable to the Alligare Flumigard at 16 ounces, but with a different active ingredient. While the Flumigard uses flumioxazin in a granule form for surface and subsurface treatment, the Semera WDG is designed for spray application after mixing. That gives you more precise control over where the chemical lands, but it requires a sprayer, unlike the throw-and-go pellets.

The key advantage here is active ingredient density — 51% means you need less product per application compared to lower-concentration formulas. Customers note that one pound covers more area than expected, making this a strong mid-range value for anyone who already owns a sprayer.

Check Price on Amazon

Spares your shoreline trees and beneficial plants while killing water lilies, because it uses a selective systemic active ingredient made for aquatic environments.

CattPlex Pro uses Imazamox as its active ingredient, which is a systemic herbicide (travels through the plant to kill the roots) designed specifically for aquatic environments. Unlike broad-spectrum options like imazapyr, imazamox is more selective — it targets common aquatic weeds like water lilies, cattails, water milfoil, pondweed, and duckweed while having a minimal impact on beneficial flora and fauna. The manufacturer says it is trusted by aquatic management professionals and helps preserve the balance of the ecosystem.

At 32 fluid ounces, the liquid volume is the same as the Alligare Ecomazapyr (32 fluid ounces), but the active ingredients are different. The CattPlex Pro covers 1,000 square feet per quart according to the specs, which makes it ideal for smaller ponds, docks, or shoreline patches. It also names water lilies directly in its description, which is reassuring if that is your primary target. The item weight is 32 ounces, matching the application volume precisely.

The trade-off is that reviewers point out it is priced higher than the other options, but they get a product specifically formulated for aquatic environments that is safer for the things you want to keep. One buyer reports that visible die-back on cattails and surface lilies appears within a week, and that the spray formulation is easy to apply with a backpack or handheld sprayer.

Check Price on Amazon

No sprayer, no mixing — just toss these 16 ounces of granules onto the water to knock back algae and young weeds within days.

This is a granular flumioxazin product, so you do not need a sprayer or mixing tank — you just broadcast the granules over the water surface. It gives rapid knockdown of filamentous algae (stringy, hair-like algae) and young terrestrial weeds, making it a fast-acting contact option. The manufacturer says to apply when weeds are young and healthy, and in sunny conditions above 65°F, as moisture activates the herbicide in the soil for residual control (continued prevention of regrowth).

At 16 ounces (1 pound), the item weight is the same as the Atticus Semera WDG (16 ounces), but the form is different — Flumigard is a granule for direct broadcast, while the Semera WDG is a water-dispersible granule for spray mixing. The Flumigard is specifically designed for both surface and subsurface treatments in lakes, ponds, canals, and around woody ornamentals. It also pairs well with systemic herbicides like glyphosate, according to the manufacturer, to boost post-emergent control.

The 1-pound bag is a smaller quantity, so unlike the 50-lb Navigate or the 5-lb SonarOne, this is best for small ponds or early-season spot treatments. Reviewers appreciate that it works fast on algae mats, but for established water lilies, you may need a systemic partner product to also kill the roots.

Check Price on Amazon

Kills weeds from the roots up without a sudden oxygen crash that can suffocate your fish, because the 5-pound bag of pellets releases the herbicide slowly over time.

SonarOne works differently from the contact killers above. It uses a slow-release pellet that sinks and disperses the herbicide through the water column over time, killing weeds systemically (through the roots). The big advantage here is safety for fish and pets — the manufacturer states it is EPA-approved and non-toxic to fish, pets, and wildlife, so it is safe for residential ponds, farms, and lakes. By killing weeds slowly rather than all at once, it prevents sudden oxygen depletion that can suffocate fish.

At 5 pounds, it is a significant step up in quantity from the 16-ounce (1-pound) bags of Flumigard and Semera WDG. The unit count is 80.0 ounces, compared to the 8.0-ounce unit count of the Atticus Semera SC — 80 ounces versus 8 ounces. It covers approximately 0.25 to 1.0 acres per 5-pound bag, making it a mid-to-large pond solution. Application is simple: just throw the pellets evenly over the pond surface — no mixing, no spraying.

The downside is that slow release means slow results. You will not see rapid leaf burn like with flumioxazin; instead, the weeds slowly wither over a couple of weeks as the chemical works through the root system. The manufacturer says it targets hydrilla, coontail, elodea, duckweed, and milfoil, among others, but water lilies are not explicitly listed in the product data — check the full label to confirm.

Check Price on Amazon

Explicitly lists water lily and spatterdock in its treatment list, in a 50-pound bag that covers 1 to 2 acres — made for lake-sized jobs the smaller products cannot handle.

This is the heavy artillery. Navigate is a 50-pound bag of granular herbicide designed for large ponds, lakes, and other freshwater habitats. It uses granule technology for controlled dispersion throughout the water, meaning you can spot-treat specific zones rather than treating an entire water body at once. The treatment list is explicit: it controls watermilfoil, waterstargrass, bladderwort, water lily, coontail, watershield, water chestnut, and spatterdock — all of which are common nuisance aquatic plants.

At 50 pounds, the item weight and unit count (800 ounces) dwarf every other product on this list. It covers approximately 1 to 2 acres per bag, making it the clear choice for large-scale problems. Unlike the SonarOne at 5 pounds which covers 0.25 to 1.0 acres, the Navigate is designed for serious infestations. The manufacturer says it is especially effective against Eurasian watermilfoil, an aggressive invasive species found nationwide, and can be used as a spot treatment for targeted zones.

The sheer size is the main barrier here — 50 pounds of granules is heavy to transport and apply by hand, and you need a significant infestation to justify the volume. Shoppers say that it works well on shoreline lily pads, but application requires careful measurement to avoid over-treating. Check state restrictions before ordering, as it cannot ship to AK, CT, FL, HI, ME, NJ, NY, VT, WA, or Canada.