During the winter when the pond surface freezes, toxic gasses are formed by decomposing organic debris. The gas is trapped for prolonged periods of time because it cannot escape through the ice cap. These gasses are very damaging to the inhabitants.
Although it is important all year, Fall is a particularly good time to clean your pond thoroughly, removing any accumulated muck from the bottom. (It is in the Fall that more debris is dropped into the pond from trees shedding leaves and blowing storms.) Cleaning will leave as little decaying potential as possible.
However, no matter how clean, there will still be gas build-up under an ice-covered pond. The best and easiest solution for ice-over is to use a pond heater or de-icer. Although "pond heaters" are not made to actually heat your pond (not like a swimming pool or aquarium), they ARE made to keep a gas exchange hole open during times of freezing surface.
Don't, under an circumstances, chip or chop away at the surface ice as this creates serious, injurious shock waves through the water.
If your pond is in the ground, keep it full of water. Turn off your pump and filter when freezing is imminent. Store the pump in a bucket of water somewhere that it won't freeze. The practice of keeping your pump wet will extend its life by preventing the O rings and seals from drying out.
Plants need some tending as winter approaches. Lift all of the plants and remove vegetation to within 2" of the crown. If your pond is deep enough that it will not freeze below the rootstock, lower your plants in their containers to the bottom - at least 30-36" in northern climates. If the pond will freeze below the rootstock, remove the plants, wrap the rootstocks in moist newspaper, cover with a plastic bag and store in a cool, dark place. Check them often enough to be sure that they stay moist. Storage in a garage or basement is usually ideal. Temperature should remain between 40-60 degrees F.
Winterizing tropical plants in northern climates is challenging at best. Sometimes it is just as economical and convenient to purchse new plants in the spring.
Feed your fish increased rations in the early autumn, then gradually cut back the amount of food as the temperature drops. Feed a lower protein food as the temperature gets cooler until you stop feeding altogether below 45 degrees F.
Leave the fish in the pond if it will not freeze solid. If the pond is above-ground, drain your pond, bring your fish into an aquarium and winterize your plants as described above.