Remove the water lily from the container or cut the container off the plant, if necessary. Wash away some of the soil and inspect the roots. Cut off any damaged or mushy roots on the water lily and any frail or dead leaves.
Obtain a container at least double the size of the present one. Some of the options include fabric pots, mesh baskets or special aquatic pots without holes.
Fill the pot one-half to two-thirds full with an aquatic soil mix. Insert as many aquatic fertilizer tabs as recommended for the size of the pot.
Place the water lily in the pot in the center for tropical lilies or angled on one side for hardy lily varieties. Spread the roots out.
Put soil around the water lily to cover the roots, but keep the crown of the plant above the soil. Never plant the water lily deeper in the soil than the plant previously grew.
Add a 1/2- to 3/4-inch layer of pea gravel on top of the soil. This keeps the soil in the container and shields the water lily plant's crown.
Water the container thoroughly and then lower it into the pond at the proper height. Place hardy lilies with 12 to 18 inches of water above the pots and tropical lilies with 6 to 12 inches.