Typically, people drain their ponds for the winter when their worried about ice damaging equipment or the pond liner itself. This is especially true in the case of particularly shallow ponds which run the risk of freezing solid all the way to the bottom. Draining your pond also typically means removing any pumps or equipment from the pond and storing them in a safe place. Pumps should be stored in water that cannot freeze, in order to prevent rubber seals from drying and/or cracking.
However, moisture is still likely to enter your pond through the winter, even if you've drained and covered it properly. Moisture can enter your pond from precipitation, runoff, or a number of other means. This moisture can freeze, and cause damage, even if you've drained your pond particularly to avoid this.