Pond pumps need to be kept submerged in water at all times to prevent the seals in the pump from drying and cracking while in storage. However, the water they're in can't be at risk of freezing, so keep it somewhere insulated like a basement or garage. When removing your pumps for winter make sure that you check them for damage or debris and clean them before storing them away. Any repairs or maintanence that needs to be made is best to do in the winter so that there's no lapse in treatment when your pond needs it most.
Winter is also a good time to replace filters, test batteries, and inspect your equipment for damage or excess wear. Do this not just for your pump, but for your aerators, filters, skimmers, and even your non-mechanical equipment like nets or pond rakes. Replacing or repairing your hardware is easier and much less disruptive during the wintertime.
