The Baltic Sea is one of the world’s largest bodies of brackish water. It has a large catchment area with high anthropogenic impact and is characterized by shallow water and a long retention time. Due to these conditions the ecosystem of the Baltic Sea is sensitive. Nutrient loads can cause dramatic increases in phytoplankton biomass which may be beneficial to some species but harmful to others. Studying phytoplankton dynamics and response to changing climate conditions is of high interest for protecting the Baltic Sea environment. To this purpose, our research group has several projects that aim to characterize populations of diverse phytoplanktonic species to better understand the impact of changing environmental conditions and the role these populations play in these shifts. Our special interest lies in the study of picophytoplankton; despite their small size, picoplankton is present in high abundances (up to 100 000 cells per ml) and are highly efficient in taking up nutrients. However, it is not yet understood what regulates the abundance and activity of picoplankton in the Baltic Sea. Understanding the seasonal dynamics of picoplankton and their interactions with other phytoplankton species such as the filamentous nitrogen fixing cyanobacteria, which cause massive blooms during summer, is of high importance for understanding the nutrient cycles of the Baltic Sea and understanding the future challenges of the ecosystem.