Picophytoplankton (<2 μm diameter) is a diverse group of picocyanobacterial and photosynthetic picoeukaryotes (PPE).Picophytoplankton contribute significantly to total phytoplankton biomassand can dominate primary production in oceans, lakes and estuaries. In the estuarine Baltic Sea, the composition of picophytoplankton is linked to the north to south salinity gradient but knowledge of the seasonal dynamics interms of abundance, biomass and diversity is largely unknown. This thesis investigated the in situ dynamics, bottom up and top down controls of picocyanobacteria (SYN; consisting of primarily Synechococcus and Cyanobium among other genuses) and PPE at two sampling stations, one coastal and one offshore. Monitoring data over three years (2018-2020) showed high biomass contribution across all seasons. Picocyanobacterial peak abundances occurred from spring to summer at the coastal station and in late-summer to autumn at the offshore station (up to 4.7 × 105 cells mL-1).Differentiation of pigment populations showed that phycoerythrin rich(PE)-SYN was the main contributor to SYN abundances except at the coastalstation during summer, when PE-SYN and phycocyanin rich (PC)-SYN had equal contributions. PPE peak abundances occurred during late summer to autumn (up to 1.1 × 10⁵ cells mL^-1 cells ml^-1). Temperature was linked topicophytoplankton growth and abundance, with PE-SYN, PCSYN and PPEadapted to different temperature ranges. Temperature also affected SYNnitrogen preference: SYN was nitrogen limited during early summer and at>15°C there was a preference for ammonium over nitrate. Clade A/B dominated the SYN community, except during summer at the coastal station when low nitrate and warm temperatures promoted S5.2 dominance. Grazing was observed to control SYN and PPE abundances and had an effect on the SYN community structure. Identification and laboratory experiments of key Synechococcus strains using a range of salinity, temperature and light conditions provided important insights into the physiological diversity of co-occurring ecotypes and links to the SYN dynamics that were observed in the field. In summary, this thesis provided novel information of picophytoplankton dynamics and community structure in the Baltic Sea. The results show that picophytoplankton play a relevant role in Baltic Sea and shows the importance of monitoring programs to understand picophytoplankton dynamics.