There are two things need to be clarified: (1) Why is only water layer on the surface frozen in freezing winter? (2) How can these creatures adapt to cold temperature?
To answer the first inquiry, thank God for the existence of water molecules on this Earth. Water seems to have a unique physic properties. Because water is transparent and allows visible light pass through, this makes sense for phototrophic organisms such as algae, cyanobacteria, seaweeds, etc. Although light can be detected as far as 1000 meters down in the ocean, the density of light reduces so much under very deep level.
Other relevant and exciting property is that when water is heated up, its density decreases at low temperature (at lower 4oC). This property explains why ice never sinks in water. In winter, the convection happens until the temperature of the upper surface of the lakes and the ponds is less than 4oC. When the convection stops, the top layer becomes frozen. At this time, this ice layer naturally prevents heat exchange between the beneath water layers and the cold environment. So, the temperature of the liquid parts of the lakes and the ponds is hard to down lower than 4oC.
In the case of fish species, the evolution gave them many capabilities for adapting to extreme conditions. Depending on species, some can migrate to warmer areas; some can change the metabolic processes to the stage of torpor to adjust to the low level of oxygen, and save energy. Recently, the scientists also found protective proteins, so-called antifreeze proteins, in the blood of the cold-water fish, which can disturb the water molecules and prevent it from forming ice-crystal. Actually, until now, there are still many things which are unclear, especially biochemical mechanisms in such ways fish can survive in cold condition.