There are several reasons to explain loss of fish over winter.  One of the most common is a phenomenon called Winterkill.  Winterkill describes a combination of factors including reduced oxygen and increased gas production resulting in the loss of fish.  The gas methane is the result of the breakdown of vegetation from the bottom layer or benthos layer in the pond.  Snow covered ponds with thick ice can become a sealed compartment resulting in fish mortality.  A January thaw or the lack thereof can be a predictor of fish loss.  Ponds that are frozen from November to April will commonly experience Winterkill.  Larger fish are most susceptible with smaller fish surviving but a complete kill may occur.  Grass Carp fish which are vegetarians may reduce vegetation present over winter and thus may help prevent winterkill.  Pond aeration which allows the gas to escape virtually eliminates fish loss.  Call for a custom pond aeration design for your pond.