How to Get Rid of Lily Pads in a Pond Naturally

Pond Academy is reader-supported. Buying through links on our site may earn us an affiliate commission. As an Amazon Associate I earn from qualifying purchases.

How To Get Rid of Water Lilies In A Pond Naturally

If your pond is being overtaken by invasive species of lilies or even native species, then it’s time to remove and control them, thus limiting the potential of them choking up your pond again.

There are several different ways to remove water lily from ponds. The best approach for you will depend on the size of your pond or lake and the size of your infestation.

Let’s start with the cheapest method of removal…

Hand Removal

Just like removing cattails and other pond weeds, you can manually remove lily pads by simply pulling them out with your bare hands.

While this may be an effective method for small ponds with a few lily pads, it can be a daunting task (and perhaps not even possible) if you have a large pond or lake with a large infestation.

Plus, pulling out lilies by hand can leave behind the rhizomes, which means the lilies will most likely sprout back up.

If you decide to go this route, try and pull up the rhizomes, as well. And be aware that you will most likely stir up sediment and debris in your pond causing it to look murky. This sediment will settle down, however, in about a day.

Plus, a little pro tip from a veteran… wear waterproof gloves with a non-slip tread. It will make the job a lot easier!

Lily Pad Removal Tools

Another natural method of lily pad removal is with the use of tools. Tools can make removing a large infestation a lot easier.

There are several different types of lily pad removal tools on the market. The best tool for you will depend on the size of your pond or lake and the size of your lily pad infestation.

Let’s find the best tool for you!

Lily Pad Removal Rake

A pond rake can help you remove lilies in several ways:

• Raking the surface of the pond, essentially ripping the lilies up and out of the water.
• Dredging the bottom of your pond, which is great for getting the roots and rhizomes out.

The latter method is preferred, as you’ll get more of the rhizomes up.

Just keep in mind, that again, you’ll be stirring up sediment causing murky pond water. If you have fish, this can be a stressful experience so you may need to remove them during this process

This can be another cheap alternative if you follow our homemade pond rake instructions. Alternatively, you can buy a pre-built pond rake, as well

Lily Pad Cutter

A lily pad cutter is essentially an aquatic weed and grass razer for ponds and lakes.

They are very effective at removing large infestations of lilies and pond weeds. And they are very simple to use; just toss the cutter out into the water, let it sink, and pull it in.

The downside of this method is it doesn’t remove the roots or rhizomes. You may want to combine this method with pond dye (see below) which will effectively block sunlight from reaching the roots and stunting their growth.

Aquatic Vegetation Groomer

An aggressive solution for large infestations, an aquatic groomer is basically a gas-powered weed whacker for underwater vegetation.

This weed whacker for water is great for removing lily pads and other vegetation up to 4 feet deep.

Of course, I’d highly recommend you remove any fish from your pond before attempting this type of lily pad removal.

Keep in mind, while the above tools can make the job easier and save you time, none of them are great at getting up the rhizomes, so you’ll most likely have to repeat the process several times a year.

Also, if you’re cutting lilies in a pond or lake, you’ll want to make sure you remove as much of the cut lily pads as possible (instead of leaving them to sink to the bottom of your pond, thus allowing them to regrow, creating pond sludge, and other problems).

Pond Liner

This isn’t an option for everybody, but installing a pond liner, or some sort of substrate (like gravel) on the floor of your pond will help control lily pads and most types of pond weeds.

This is a lot easier to do if you have yet to build your pond. For those with existing ponds or lakes that don’t have a liner or substrate, you can add rock rip-rap 2 to 3 feet above and below the waterline. And/or you can weigh down a large pond liner on the bottom of the pond (and perforate it to allow for gases to escape underneath the liner).

Pond Fish

Certain species of pond fish enjoy eating water lilies, which is why some pond owners try to use them to control lily pads from taking over their pond.

Fish that will eat lily pads include Koi fish, goldfish, and grass carp.

With that said, you can’t control the types of plants that your fish will be eating, so they may eat pond plants that you want in your pond.

And before you try adding grass carp to your pond, check that you can legally do so in your state. Even if you can keep in mind that grass carp can eat 2-3 times their body weight in vegetation per day! So, only add 5 carp per vegetated acre to control lilies and other vegetation.

Pond Cover

Covering the infected area of your pond with a liner or even a window screen will effectively kill water lilies.

Basically, you take your liner or screen and lay it on top of the lilies in your pond (or any floating or submerged plants). This will block essential sunlight from reaching the plants and compress them, as well, killing them off in a matter of weeks.

You can do this one area at a time, simply repeating the process in a new area until the lilies are gone.

Pond Dye

Working on the same principle as a cover, pond dye effectively shades the plants from essential sunlight, killing them off in a matter of weeks. This works best when the dye has been added to your pond in early Spring before plants have started growing or have reached the surface.

Best Herbicide For Water Lilies

If none of the above natural methods have worked, then we can move on to chemical removal methods.

Here are two of the most popular and effective aquatic herbicides on the market today.

Shoreline Defense

Shoreline Defense by Pond Logic is a broad spectrum weed killer that works great on water lilies, cattails, and other emergent pond weeds.

It’s easy to apply and it kills down to the roots, ensuring that the lilies won’t grow back.

Rodeo Lily Pad Killer

Rodeo Aquatic herbicide is a Glyphosate-based weed killer designed to kill lilies and other pond weeds down to the roots for long-lasting control.

Rodeo herbicide works best on lilies once the plants are mature. And it’s concentrated, so remember to follow the directions and mix it properly according to the label.

Rodeo herbicide is registered in every state except Alaska (at the time of this writing)

Pond Lily Removal FAQ

Are Lily Pads Good for Ponds?

Lily pads are good for ponds in moderate amounts as they provide shade for your pond fish and other inhabitants, they are a food source for nearby animals including deer, waterfowl and beavers, plus they are aesthetically pleasing.

However, if left unmanaged, they can cause issues for your pond. They can rapidly grow and out-compete other plants, deplete oxygen levels, and as they die off, they can create water-quality issues.

So, as long as your pond isn’t overtaken by lily pads, they are a great addition to any pond!

Does Salt Kill Lily Pads?

Yes, salt will kill lily pads.

Unfortunately, it has the potential of damaging and killing the other plants and wildlife in your pond if not dosed correctly.

We don’t typically recommend using salt, but if you decide to go this route, be sure to use a high-quality pond salt.

You’ll want to use a saline tester to make sure the salt levels don’t get too high.

And I’d remove any pond fish and/or plants (the ones you want to keep) during this process.

What Eats Lily Pads in a Pond?

A lot of different wildlife, including animals that live in and out of your pond, enjoy munching on water lilies!

Fish like koi, goldfish, and grass carp will sometimes eat lilies. Nearby wildlife like beavers, deer, waterfowl, ducks, and more enjoy eating lilies out of ponds. And even aquatic leaf beetles and aphids will eat lilies.

Will Roundup Kill Lily Pads?

Yes, Roundup should kill lily pads. However, be sure to only use a chemical weed killer that is labeled safe for aquatic use. Roundup does now have a product designed for aquatic use called Roundup Custom Herbicide, which has an active ingredient of Glyphosate. It’s labeled as being safe for aquatic organisms according to the EPA.

How Do You Kill Lily Pads Without Harming Fish?

You can safely kill lily pads without harming fish using any of the natural removal methods, including hand removal, using certain tools like a pond rake or lily pad cutter, adding pond dye (especially in early Spring), or simply introducing more fish like koi that will consume the lily pads.