Lily pads are ethereally gorgeous; delicate, magical...and ravenous. A small, healthy patch can take over an entire lake faster than you would believe possible. It's not hard to kill lily pads, but it does take some work. Many experts recommend hiring professionals, but if you have the time and the energy, you can do it yourself, or with a helper. Killing lily pads is much like killing weeds; you just need the right tools and materials.
Rake as many of the lily pads off of the surface as you can. Use a rowboat or canoe if the lake is fairly large, and have a helper to steady the craft as you use the rake. Avoid boats with engines so you don't stir up the water or tangle the roots too much.
Use a garden sprayer to spray a glyphosate-based aquatic herbicide on the lily pads. Do one small area at a time, because decomposing plants can steal oxygen from the fish in the lake.
Read the directions on the label to see how long you can expect to wait for the herbicide to do its work. At that time, use your rake to pull all of the dead lily pads out of the lake that you can, making sure to get as much of the roots as possible.
Wait 2 to 3 weeks and then spray another small section; let the herbicide work its way down into the lily pad roots, and then remove the dead ones. This can take awhile in a large lake, but trying to remove them all at once is not a do-it-yourself job, and it's not good for the ecosystem of the lake.