Remove debris in the water pond, including dying plants and leaves.
Stop fertilizing the water lilies as soon as the weather cools slightly in the fall. This is when the plants start entering dormancy; the lack of fertilizer halts growth and root development. Remove dying foliage to prevent it from falling into the water.
Take tropical water lilies out of the water but keep the container intact.
Prune the largest leaves from the plant. Remove dying or damaged foliage. The plant needs to be compact enough to fit into a lined pond or aquarium in a protected location, such as a basement or house.
Place the plant pot in an aquarium or pond indoors. Ideally, choose a location with a consistent temperature above 60 F; the temperature shouldn't drop below 50 F.
Allow the water to evaporate from the indoor aquarium or pond over the next few months. This is the dormant period for the lily.
Cover the water pond with netting to keep falling leaves from getting into the water. If debris already fell in the pond, remove all plants and wildlife to a holding container. Drain the water and clean out all debris. Refill with water. Get the pH and temperature back to where it was before the cleaning, then replace the wildlife.
Pour warm water into the holding tank in the spring as the tropical water lily comes out of dormancy. Wait a couple of weeks until the weather warms up, then plant the lily in a new container. Add fresh soil and fertilizer, following your regimen from the previous year. Return the pot to the outdoor pond.