In late summer or early fall, stop fertilizing your water lilies entirely. This lets their system know that cold weather is approaching, and will encourage the plant to grow tubers which provide food for them throughout the winter. This also prepares the plant to enter a period of dormancy, which slows down their energy use and need for food.
For hardy water lilies, move them to the depest parts of your pond. This protects them from the cycles of melting and refreezing that are more common in shallower water. Tropical water lilies will need to be stored indoors where they're protected from the coldest parts of the year.
