The 5-year-long (2001–2005) studies of the winter thermal structure and the dissolved oxygen (DO) dynamics in Lake Vendyurskoe, Russia, a typical boreal shallow mesotrophic lake of glacial origin, revealed still poorly studied features of lake-wide dynamics, such as net lateral heat flux towards deeper parts of a lake and development of the anaerobic zone over the deepest points of the lake basin. We estimated magnitude of the heat transport along the bottom slope based on scaling analysis. The seasonal changes in DO concentration appear to be controlled mostly by biochemical consumption. We identify four factors controlling the extent of anoxic zones in shallow ice-covered lakes: (1) the amount of organic matter stored in the bottom layers, including the sediments surface during the autumnal bloom; (2) the length of the ice-covered period; (3) heat content of bottom sediments; and (4) the initial water temperatures at the time of the ice cover formation.