The thermal stratification of the upper water layers in the Baltic Sea varies seasonally in response to the annual cycle of solar heating and wind-induced mixing. In winter, the stratification down to the halocline is almost completely eroded by convection and strong wind mixing. Monthly averaged temperature profiles obtained from the ICES hydrographic database were used to study the long-term variability (1950 to 2005) of winter water mass formation in different deep basins of the Baltic Sea east of the island of Bornholm. Besides strong interannual variability of deep winter water temperatures, the last two decades show a positive trend (increase of 1-1.5°C). Correlations of winter surface temperatures to temperatures of the winter water body located directly above or within the top of the halocline were strongly positive until the autumn months. Such a close coupling allows sea surface temperatures in winter to be used to forecast the seasonal development of the thermal signature in deeper layers with a high degree of confidence. The most significant impact of winter sea surface temperatures on the thermal signature in this depth range can be assigned to February/March. Stronger solar heating during spring and summer results in thermal stratification of the water column leading to a complete decoupling of surface and deep winter water temperatures. Based on laboratory experiments, temperature-dependent relationships were utilised to analyse interannual variations of biological processes with special emphasis on the upper trophic levels (e.g., stage-specific developmental rates of zooplankton and survival rates of fish eggs).