Lily pads are great-in moderation. However, what starts out as a great way to shade your fish and keep your pond pretty and cool during the summer months can quickly explode into a choking mess of aquatic foliage if you are not careful. Getting rid of lily pads completely can seriously hurt your fish population, so you may want to control them rather than eliminate them entirely.
Consider moving in some sterile pond carp. These fish love to eat aquatic vegetation and can quickly mow down a rampant lily pad population. However, they will not eliminate the plants entirely, so this is a good option if you want to keep a few, but a bad option if you just want the entire area clear. Start with 1 to 3 small carp per acre of your pond, then add 1 or 2 new carp each year depending on how you like the results.
Mix up a cleaning solution. Spraying the lily pads with a mild dish detergent will make them far more susceptible to your organic aquacide because the detergent will break down the wax on the leaves. Fill a spray bottle 3/4 full of warm water and add 5 drops of dish detergent. Spray the detergent mixture on the leaves to break down the wax.
Mix up your aquacide solution. Check the instructions and all of the warnings to make sure that your herbicide will not hurt your fish. Generally you will dilute the herbicide with water, but you need to be very careful to adhere closely to the manufacturer's instructions because every brand has different concentrations and high concentrations of even an organic product can harm aquatic life if used incorrectly.
Apply the herbicide directly to the lily pads. If they are very thick, then you can just spray it over the pond. However, if you have a small pond, you should do your best to apply the aquacide only to the lily pads and not hit any more water or surrounding vegetation than you have to.
Remove the vegetation as it dies. You will need to fish out the dead lily pads or they will clog up a small pond. You can use a long-handled rake or your hands. If you do not get all of the debris, it is okay, but try to keep major clumps from gumming up your works.