Winter care for water lilies varies depending on whether the types you are growing in your water garden are tropical or hardy natives. Most native varieties can be placed in the deepest part of the water garden pond to overwinter; tropical varieties must be removed from the pond and placed in winter storage above freezing except in the very warmest climates. However, native varieties will not be harmed by cool winter storage, so bringing your water lilies in to a sheltered winter location is the safest bet to ensure they will bloom again the following year.
Fill a 5-gallon bucket halfway with clean playground sand. Add rainwater or well water until the sand is moistened but not saturated.
Remove your water lily from your water garden in late fall, after its growth has died back. Keep it in its pot, if it is planted in one.
Cut away dead stems and foliage with pruners. Trim back any dead and decaying root ends.
Place the water lily (and its pot if it is in one) in the 5-gallon bucket. Fill the bucket the remainder of the way with clean playground sand and water it until it is moist.
Place the bucket in a protected location where temperatures will be below 60 degrees but higher than 32 degrees for the duration of the winter. Check the moisture of the sand about once every other week, and add water if it has dried out.
Move the bucket to progressively warmer locations in the early spring, being sure to keep the sand moist. Replace the aquatic potting medium in your water lily pot and add one or two aquatic fertilizer tablets to the medium before returning your water lily to your water garden after the water has thawed in the spring.