The winter season is often described as a dormant season, although the sea ice is a habitat for diverse and active communities in polar and subpolar areas. These areas are subject to changing environmental conditions due to the global warming, and temporal and spatial studies are required in order to understand changes in biodiversity and the processes organisms perform in these ecosystems. Here, we delineate the microalgal succession in the northern Baltic Sea during the cold-water season using weekly-collected time-series data. The samples were obtained from the water column between October 2012 and May 2013 and from the sea ice during the ice-covered season. The biomass in the water column remained low until the end of the ice-covered season and was dominated by small flagellates and dinoflagellates. The young ice community resembled the water column community, but due to lower species richness compared to water column, indicated a partly selective concentrating mechanism during the ice formation. The biomass increased in the ice and water column during the spring and the community changed from flagellate-dominated to diatom- and dinoflagellate-dominated community. In addition, the spring community forms a separate community indicating that the sea ice algae do not contribute to the spring bloom community. This novel data shows that the wintertime is not dormant, but has five distinguished groups based on the microalgae assemblages.