The water lily (Nymphaea odorata) is a common pond plant known for its massive, sweet-smelling pink, red, yellow or purple flowers. Though typically grown for ornamental purposes, the water lily can become a nuisance if not controlled, quickly overtaking a pond and choking out other plants.
Remove the water lilies manually. This is ideal for killing small patches of water lilies or to help control large patches of lilies. Scoop the plants out by hand or with a net and lay them in the sun to dry and kill them. Cut dense patches with pruning shears to aid removal.
Drag a hard-tined rake along the pond's bottom to remove the water lilies' roots and underwater stalks after removing its surface growths. Lay these in the sun to kill them, too. Dispose of the plants or add them to your garden's compost or mulch pile.
Spray the surface water lilies with a glyphosate-based aquatic herbicide, available from most nurseries and garden stores. Example products include AquaMaster, Glyfos Aquatic and Rodeo. This method is ideal for wide-scale lily infestations. Mist onto the lily plants according to the manufacturer's guidelines, as toxicity varies by product. Wait seven to 10 days for the lilies to die. Repeat the herbicide application to kill any you may have missed.
Use a granular aquatic herbicide that contains fluridone or 2,4-D, such as Sonar or AquaKleen. Granular herbicides are an alternative to the more labor-intensive sprays, as they do not need to be applied directly on every plant. Such granule-based products should only be used in enclosed ponds that have little water movement to avoid dilution. Scatter the granules into the pond water near the water lilies according to the manufacturer's instructions, as potency varies widely by brand.
Prevent water lilies from taking over again if you choose to replant the species in your pond. Contain the water lilies to a sunken aquatic pot to limit the plants' ability to spread wildly. Monitor the area to immediately prune back lilies that may begin spreading to areas in which you don't want them.