If you live where the temperature drops below freezing in the wintertime and have a small pond, you will need to store your water lilies to prevent them from freezing. If your pond is over six feet deep, you can leave them in your pond, but if not, you will need to remove the plants and bring them indoors. You can store them in a basement or storage closet as long as they are completely covered with water. They should be in a covered container, so that the light does not stimulate them to grow. After the last frost, you can return them to your pond.