Covering your koi pond in the winter will help keep temperatures warm and prevent leaves or debris from falling into the water. A cover also may help prevent predators from eating your fish. It's important to prevent as much debris from entering your pond as possible, especially during the winter. As organic material decomposes, it releases toxic gases in the form of sulfur dioxide, ammonia, and CO2. These gases can suffocate fish and plant life and severely reduce your water quality. Typically, these gases escape from the water's surface into the open air. However, if your pond is completely encased in ice, theres nowhere for these gases to go.
One of the best ways to prevent this process from occuring is by removing as much organic material from the pond as possible. This will involve scooping out sludge and muck during the late fall and utilizing covers to prevent more debris from entering the water.