The Baltic Sea is a unique brackish ecosystem with a pronounced gradient in temperature, salinity, and nutrient limitation from north to south. In the northern regions, such as the Bothnian Bay and Bothnian Sea, conditions resemble freshwater ecosystems with lower temperatures and salinity, where phosphorus (P) is the limiting nutrient. Moving towards the Baltic Proper and southern areas, characteristics become more marine-like with higher temperatures and salinity, shifting nitrogen as the limiting factor. Eutrophication affects the southern basins due to significant nutrient inputs from its extensive drainage area, resulting in seasonal phytoplankton blooms dominated by dinoflagellates and diatoms in spring, cyanobacteria in summer, and small flagellates in autumn. Climate change forecasts indicate rising temperatures could reduce salinity alongside increase P release from sediments—factors likely to worsen eutrophication with more filamentous cyanobacteria and increased microbial P recycling post-blooms. Despite these challenges, there is limited focus on how microbial plankton communities strategize P acquisition. This thesis addresses this gap by examining interactions among phytoplankton and bacterioplankton across different Baltic Sea basins. The interplay between different plankton size-classes, stoichiometry and P-acquisition strategies are crucial to understand factors promoting their co-existence in diverse ecological landscapes. Seasonal dynamics of phytoplankton across three basins—Linnaeus Microbial Observatory (LMO) in the Baltic Proper, Bothnian Bay, and Bothnian Sea revealed significant spatial-temporal variations. In spring, northern diatoms dominance contrast with dinoflagellates prevalence in the Baltic Proper; cyanobacteria become prominent during summer except in Bothnian Bay. Despite the differences in community composition, size-fraction protocols and elemental stoichiometry emphasize nanoplankton (<20µm) and picoplankton (<3µm) as major players in nutrient uptake processes throughout these basins. Metatranscriptomic analyses suggest that despite different compositions among basins, microbial planktonic communities shared similar P acquisition mechanisms. Gene expression associated with the membrane remodelling appears as the main mechanism in eukaryotes, it emerges as an essential secondary process in prokaryotes with transporters having a pivotal role. This highlights the critical function of cellular P pools in response to P deficiency, ensuring cellular adaptability and survival despite fluctuating conditions. Overarching trends emerged community-wide, but nuanced differences between prokaryotes (bacteria) and eukaryotes (phytoplankton) highlighted their capacity for adaptation within the different basins. This complex interplay between environmental drivers and biological adaptability deepens comprehension of ecological dynamics within marine ecosystems like the Baltic Sea.