Seismic study of transition zones in Arctic regions in summer is troublesome because of the presence of large areas covered by shallow waters. The winter is much more convenient with respect to logistic processes and implementation of seismic observations. But at winter there is a complicating factor - intensive noise when an acquisition is installed on the ice, covering shallow waters. The paper presents results of careful numerical study of this noise and brings to the light the main reasons of its generation. It is caused by the conversion of flexural waves on heterogeneities of ice bottom. Some ways to reduce this noise are proposed and discussed.