All hardy water lilies overwinter perfectly well, if their rhizomes do not freeze completely. 
Since water lilies come in different sizes – miniature, small, medium and large – their winter care primarily depends on their vigor and type/depth of your water feature. While miniature water lilies are best grown in shallow waters, their more vigorous counterparts prefer the deeper end of a pond.
In natural ponds large water lilies are generally planted 1-1.5 metres deep. The thickness of the ice layer on large ponds rarely exceeds 1 metre even in the most severe winters, when temperature keeps at around -30oC for a couple of weeks, so the water lilies are safe at the bottom of large water features.
When large water lilies are planted less than 1 metre deep, or if a particular water feature tends to freeze to the very bottom in winter, the safest way is to plant them in aquatic baskets. When the winter sets in, they should be moved either into the deeper end of the pond or a cool cellar (basement), whichever is more appropriate in your case. The basket with the water lily should be stored submerged in a container filled with water. The same rules apply to the medium, small or miniature water lilies. If you do not have a basement, after being carefully rinsed and soaked in the Previcur fungicide, rhizomes could be stored in damp peat or moss in the fridge.
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