How to Get Rid of Lily Pads in Ponds (Best Tools & Methods)

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How to Get Rid of Lily Pads in Ponds & Lakes 2022 (Most Effective Tools)

how to remove lily pads
Lily pads may look aesthetic, but they can quickly become invasive and take over a pond or lake system. Public domain.

Lily pads are often viewed as a positive and beautiful part of aquatic ecosystems. Their leaves (pads) provide valuable shade, habitat, and cover for many water species like fish and frogs, while their vibrant flowers attract pollinators and are in general aesthetically pleasing. Their seeds are consumed readily by deer, beaver, muskrat, and waterfowl.

However, depending on your location there are multiple species of invasive lily pads that can be detrimental to ecosystem health if left unchecked. Even native species, like the American white water lily (Nymphaea odorataa aiton), can sometimes become overgrown and choke up ponds and lakes with their extensive mat-like rhizome root systems, consequently out-competing other vegetation, impeding fish movement, depleting dissolved oxygen, and over time lessening biodiversity. Wildlife managers usually recommend that lily pads only cover a maximum of 25% of a water body.

With over 40 species, it can be difficult to distinguish native from non-native water lilies – for example, spatterdock (Nuphar lutea), or cow lily, produces yellow flowers and is considered invasive in Michigan and much of the Midwestern U.S., but below the Missouri River is considered a native species. Yellow floating heart (Nymphoides peltata) is only native in Asia and Europe.

Your best bet is to do some research and determine which lily pad species are native and non-native to your region. Regardless, there are a variety of methods available to remove invasives as well as to keep the native species in check. These we’ve listed below with the general pros and cons of each method:-

The Best Lily Pad Removal Tools & Methods

1) Hand Pulling Lilies

Similar to cattail removal methods, you can manually pull up lily pads. While the cheapest method, it’s not always the most effective – pulling them up by hand can often leave rhizomes behind, meaning that the lilies will simply resprout. As such, pulling is just a temporary control method. It can also be quite difficult work, especially if you’re trying to manually pull up lilies from across a very large lake or pond. Often times combining pulling with other methods will provide better (and easier) results when it comes to lily pad control.

2) Raking Lilies

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Utilizing a hard-tined gardening rake or specialised aquatic rake and dragging it along the bottom of the pond or lake is more likely to remove rhizomes than hand pulling, but can be time consuming and difficult. You could also dredge along the bottom of the water body to fully remove all rhizomes. Keep in mind that both of these methods will stir up sediment, and so you might need to remove your fish and other pond inhabitants while using either of these approaches.

3) Cutting Lilies

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Typically conducted on smaller water bodies, such as in ponds, you can cut water lilies just below the water line using shears or an aquatic weed whacker. However, this is very temporary and will need to be repeated several times during the year, as it won’t kill off the rhizomes and the lilies will continue to grow.

You’ll also have to remove any of the dead vegetation from the water to prevent oxygen depletion and algae growth. The perk here is that there is little to no impact to your fish or water quality, and it’s much easier work in comparison to manual pulling and raking, especially if using a specialized aquatic weed cutter.

4) Creating Shade

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A fairly simple control method, shading involves placing a large piece of black plastic sheeting over the area of lily pads. This will prevent sunlight from getting through, and over time the plants will die. However, rhizomes are fairly hardy and can exist in dormancy for a time, meaning there is potential for the lilies to recover after using this method.

This may be more successful when used in conjunction with other control methods. You also shouldn’t use this technique if lily pads are present over a substantial part of the water body, as too much shade from the cover can negatively impact fish and any desirable vegetation that is present.

If you’re trying to control lily pads in a garden pond, installing a shade sail can help to greatly reduce their growth rate while you actively work to remove them with other methods. You can also check out our in-depth guide on how to shade a pond and recommended products here.

5) Plastic or Gravel Lining

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If your pond or lake has a well-established lily pad population, you may need to resort to heavier duty mechanical removal methods. Bulldozers, aquatic cutters, and aquatic mowers are all effective approaches that provide quick and long-term results, but in small water bodies like ponds fish will need to be removed to prevent adversely impacting them. In a larger lake, the fish will ideally be able to temporarily seek shelter elsewhere in the water.

7) Pond Fish!

koi eat lily pads
Some fish, koi in particular, can help control lily pads by munching on them. Public domain.

Some fish species love munching on water lilies, and while this biological control method won’t eliminate a lily pad population, it will help to keep it in check. As such, using fish is best suited for simply controlling native lily pads. Native lilies do provide beneficial food and habitat for a variety of wildlife species and removing them altogether could damage your fish population, while invasives should be eradicated completely.

Koi, goldfish, and grass carp are all known to eat the leaves and occasionally the roots of water lilies. Of these, grass carp are considered the most effective at controlling lily pad populations. However, it should be noted that while grass carp are cheap, they hail from China and are considered non-native in North America and Europe. Because of this, you may need to obtain a permit in order to have them in your pond or lake.

Some areas, like Florida, require that you use sterile (known as triploid) grass carp to prevent them from breeding and overtaking other fish species, and 32 out of the 50 states have made them entirely illegal to possess. They also grow in accordance to the water body size, meaning that in large water bodies with plenty of food, they have been known to reach several feet and 50-plus pounds in size, but average closer to 15 pounds in ponds. They are also likely to also nibble on other plants, such as water hyacinth, which may or may not be advantageous depending on your personal goals. Start off with one or two juvenile, less than 1-foot-long grass carp per approximately 65,000 gallons.

Controlling Lily Pads with Chemicals – A Good Option?

We really can’t state this enough – anything that is designed to kill or harm one thing is likely to kill or harm other things as well. With this in mind, chemicals should always be used as a last resort, and in strict accordance with labels and regulations. Do some research or contact your local environmental agency to learn which control methods are allowed where you live, and the regulations associated with them.

1) Glyphosate

glyphosate kills lily padsAs mentioned in previous articles, glyphosate herbicides specifically approved for water works well with aquatic vegetation removal. As a systemic chemical, glyphosate works its way throughout the entire plant, roots and all. Approved by the EPA, glyphosates are the general go-to for water use, as it does not persist in the environment and is considered generally safe for fish and wildlife as long as label instructions and proper dosages are followed. Aquapro, Refuge, Aquamaster, and Rodeo are popular liquid glyphosate brands that are approved for water use.

2) Imazapyr (Licensed Use Only)

Imazapyr to control aquatic weedsAlso used to control phragmites, imazapyr is incredibly potent, non-selective (it’ll kill just about anything that it comes in contact with), and as such is sure to eliminate lily pads. However, as mentioned in our previous phragmites control article, imazapyr persists in soil and water, is quite toxic, and will likely kill off native plants and potentially harm fish and wildlife as well. This chemical requires a license to use (you could either obtain this yourself or hire a professional) and should be applied with great care in accordance with the label. The only variety of imazapyr that can be used in aquatic systems is Habitat, and works best with a surfactant that will reduce surface tension so that imazapyr will more readily disperse into the water rather than concentrating in one area.

3) Herbicide Tablets

Herbicide (otherwise known as aquacide) tablets are quite concentrated, selective (meaning that they generally only kill what you want them to), and are designed more so to target and kill roots – this is perfect for aquatic plants that reproduce using rhizomes, like lily pads. Rather than diluting throughout the water body, tablets will sink into the root bed, release the herbicide slowly over a period of days as the tablet dissolves, and are less likely to damage other plants than liquid herbicides.

As the water lily grows, the roots directly absorb the herbicide sitting atop them and distribute it throughout the plant. In most cases, the entire plant dies after about a week. You will have to manually remove the dead vegetation, as otherwise it will sit at the bottom of your lake or pond and use up vital oxygen as decomposition takes place. In terms of chemicals, these little marble-sized tablets may be the most efficient and least harmful approach to managing your lily pad population.

29 thoughts on “How to Get Rid of Lily Pads in Ponds (Best Tools & Methods)”

    • Hi Tami,

      I can’t really advise on that, as it would likely depend on many different factors, such as water volume, chemical concentration, herbicide type, and even the species of animals drinking. The best way to get an answer would probably be to consult the label of the product to see if there is any advise, or contact the manufacturer of the product directly and explain your specific situation to them.

      In most situations, it would be safer to simply avoid chemical usage if animals and wildlife drink from the same source and opt for alternative methods of removal instead.

  1. Hi,I’m trying to control not eliminate all of my lily’s in a fishing pond and it would be extremely helpful if you could advise me on what’s best to use that won’t harm my fish,most non chemical options are difficult as the roots are between 6 and 10 ft deep
    Thank you

    • Hi Danny,

      How large is the fishing pond exactly? Also, what kind of fish do you have? Those lilies are pretty deep, and if they’re already well established over a large surface area, I think controlling will be very difficult without more extreme measures (i.e., draining/dredging, liners, chemicals etc.).

  2. I have a 1acre pond that is about 12 feet deep in center. It is taken over by lilies and cattails. I would like to fish it, but is currently impossible. What is the most cost effective / efficient way to clear it (or sections). Fish include catfish, bass, perch and I’m sure others

    • Hi LW,

      Apologies for such a very late response!

      In terms of being cost effective while maintaining efficiency, I would suggest using either an aquatic weed wacker or aquatic weed rake (slightly more expensive options), or aquatic sheers (less expensive but more time-intensive). Either of these will involve cutting the lilies and cattails to a couple of inches below the water’s surface. Since both of these plants sprout via rhizomes, it’s a temporary method that will have to be repeated several times a year, depending on the growing season. You can use a combined approach of also applying aquatic glyphosate (very carefully following dosage instructions on the label). Try cutting back the lilies and cattails, wait a day or two, and then apply the glyphosate. This waiting period means the plants will begin the healing process, in which they focus on bringing nutrients into their root systems and then disperse them in concentrated amounts to areas that are cut/injured. Once you apply the glyphosate, it will be drawn directly into the plant’s root system. Only treat one half of your pond at a time, to prevent too much plant kill off at one time as this alters dissolved oxygen content in the pond. Treat half of the pond, wait a couple of days for your fish to adjust and settle, and then treat the other half. This method should have the least amount of impact on your fish possible while also fairly effectively taking care of your plant issue. Be aware that other plants may be impacted if you go with the chemical route!

      Hope that helped! Thanks for reading and commenting.

  3. I am searching for information and potential usage for lily pads that are a very evasive in an area located in the Philippines. Are there any usages for them such as compost or other avenues to assist locals manage their waters ways.

    • Hi Tommy,

      For that large of a pond, removing that many lilies will likely be a pretty daunting task! I would urge you to remove as many as you can by using an aquatic rake or dredging, but you’d have to remove any fish if possible since both of these will stir up sediment. Alternatively, you can cut the lilies to below the water’s surface, and then treat with an aquatic herbicide. Glyphosate is the safest option for any fish and other plants that are present, and if treated right after cutting the lilies, they’re more likely to soak up the herbicide as they try to heal and transfer it into their root systems. You’ll likely have to use a fair amount for this large of a pond, so again you may want to remove fish to a safe location temporarily if possible. An aquatic mower, if you have access to one, is a decent option as well.

      Hope that this helps, and best of luck!

      • I have about a 3 acre pond and it has lilies clear around it out about 15 feet. I have used chemical glyphosate for past couple years and can’t get them under control. I was wanting to do the cover method with tarps and use pond dye to prevent UV light transfer. How long would I need to keep the tarp over them to kill them before I move it down and keep killing them as I work my way around the pond? Or is this not something that will work

        • Use grass carp and talapia, takes time, but they will clean a pond out! Used them on a one to two acre pond, and now several years it is Completely Clean, infant too clean, you can still see the carp occasionally, they are about 3 foot long now, and were only about 6 to 8 inches long when placed into pond! They work, takes time, Talapia eat Algae and pond scum, Grass carp eat plant, this works but takes a few years

        • Also, it will take time, but when those grass carp get hungry, they will eat pretty much anything, as most vegetation is now gone, they chomp on grass that shredder throws into pond, while cutting with tractor! Carp must be sterilized type, and for 3 acres, I would get 15 to 20 of them, and give them say 5 years,

  4. I have a 3 to 4 acre pond with a bad problem with duckweed and milfoil. What would be the best stuff to eradicate these underwater plants?

    • Hi Chuck,

      You can manually rake or cut them, but since you have an extensive problem with both plants, they likely have established root systems. Though we don’t advise using herbicides as a primary solution as anything designed to kill one thing can of course harm others (like your fish), there are a few active herbicide ingredients that have been found to be really effective in controlling all parts of milfoil and duckweed, including the roots. These are: Diquat, Carfentrazone, Penoxsolam, Triclopyr, and 2,4-D. All of these except for Diquat are systemic herbicides, so the they will disperse throughout the entire plant rather than only killing off the leaves. Diquat is a contact herbicide, so it’ll kill the parts it comes into contact with but probably won’t do much against the roots. If you decide to go the chemical route, be sure to get an aquatic form of the herbicide, so that it’s water soluble and will not be nearly as likely to harm the rest of your pond!

      Otherwise, you can drain the pond and manually dig, bulldoze, or dredge out the bottom to remove the roots. This is intensive, but it’ll take care of the problem without the use of chemicals. Unfortunately, milfoil in particular is very aggressive and there aren’t any natural controls for it – fish and insects don’t really seem to enjoy eating it, bacteria doesn’t just break it down, and so that leaves herbicides or removing all of the roots by draining the pond.

  5. Our lake association is currently partially draining our lake as they think it will kill off the lily pads. This has left the lake very low and is a problem for the cottage owners. I’ve argues that Lilly pad roots are hearty and do not die off during the winter as they are still in mud.

    Am I right? Or will this kill the roots?

    • Hi Wendy,

      Unfortunately, many lake associations do not actually have environmental professionals on their boards. You are correct in that partially draining the lake will not kill the lily pads; it is likely to, however, adversely impact fish, newts, turtles, and other plants in the lake. As you said, their rhizomes are quite hardy. They’d have to be completely dried out for quite some time, and partially draining the lake will not do this.

  6. Can you tell me where the statement “Most wildlife managers say lily pads should not cover in excess I 25% if a pond” was taken from? Our wetlands people in mn won’t consider that “ fact” when I ask about controlling them in my pond. Probably 90% lily pad coverage .

    • Hi Greg,

      Apologies for the delayed reply. The statement is a product of many collective years of aquaculture, pond maintenance, and wildlife ecology experience between all of us at Pond Informer. This site is based in the UK, which can cause some discrepancies in recommended actions, as well, since environmental entities and their regulations differ around the world. Unfortunately, while it is best that lily pads don’t cover more than 25% of a pond (no matter where you live) due to a variety of factors (if there are too many, they decrease water flow, block sunlight, block fish routes, etc.), some companies/organizations may lack the funding and/or manpower to remove them as they’re a pretty persistent issue in many wetlands, ponds, etc. throughout the midwest. If controlling them needs to involve the use of chemicals (likely, given you mentioned most of the pond is covered with lily pads), they may be hesitant to want to administer that much herbicide for multiple years, in addition to manual cutting and removal. It also depends on where their primary interests lie – some wetland managers may focus more on wildlife, some on plants, some on human impacts, and so on. These are all, of course, tied together. Or, in their minds, they may have “bigger fish to fry.” An unfortunate reality right now is that environmental organizations, whether state, federal, or private, are incredibly overworked and underfunded. While most of us in the environmental field want to help everything, we can’t. My guess is that the people you consulted in Minnesota are having to carefully select projects based on time, manpower, funding, and a variety of other factors. Have you tried contacting any other entities? Alternatively, you could try obtaining the permits yourself to manage the lily pads.

      This is likely not the response that you were hoping for, but hopefully it offers some insight.

    • Hi Sandy,

      Sorry about the delayed response!

      Lily pads are unfortunately quite hardy thanks to their thick rhizomes. These rhizomes can remain dormant beneath the ground for several years, and may give rise to new lilies once water is introduced again. Draining the pond for a while will help to slow them down, certainly. You may consider manually removing any rhizomes you’re able to dig up and find while the pond is drained, and/or lining the pond with a thick liner to prevent them from being able to come back again.

  7. If I use chemicals to kill water lilies that are covering about 45% of our lake do I need to figure out a way to get rid of the vegetation that dies and its impact on the ecosystem of the lake. We live in Missouri and winter can be negative temps so the roots are the only part of the plant that overwinter. Is the natural decaying vegetation each year detrimental to the lake ecosystem? if so, what is the best way to minimize this problem?

  8. I’m deactivating my pond for safety reasons. This was a pond I installed about 28 years ago. But with grandkids and new puppy it needs to go. I have drained it by puncturing the liner and removed the containers. I have cut up the rhizomes. If I now cover it with 2’ of soil will that eventually kill off the water lilies and supply nutrients to the garden in plan to put there

    • Hi William,

      Covering what’s left of the water lilies with soil should be enough to kill them off within a month or two! I would wait at least a month before planting the garden, if possible, particularly if you intend on watering it often as water lilies have been known to grow in consistently damp soil as marginal plants.

  9. Hi, I’ve got a approximate 35 acre pond that has lily pads covering about 40% of it. Put 9 grass carp in it last year and will put more in it this year but would like to do more. It’s got a good established fish population now and don’t want to arm it. Would getting a lot more carp for the pond or should I try something else? Thanks for any help you might offer!


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