Leaving some ice and snow atop your pond helps insulate your pond and protect your fish from predators. When water temperatures dip below 50 degrees Farenheit, fish naturally enter a hibernation-like state called torpor. As their metabolism slows, fish move very slowly and are less alert, leaving them vulnerable to wintertime predators like herons or raccoons. When the pond is largely protected by a sheet of ice and fish are relaxing in the deepest areas, they're a lot safer. A layer of ice also serves as an insulator and protects your pond's residents from rapid temperature fluctuations, which can stress or even kill your fish.
There are some concerns with allowing your pond to completely ice over, however. It's essential to create and maintain a hole where oxygen can enter, and toxic gases produced by decomposing organic matter can escape. This hole should be located in a shallow section of your pond. You'll need to maintain it through the winter by employing a deicer or by periodically using boiling water to melt any ice that's threatening to seal the hole.
