The oceans harbour an immense diversity of microorganisms that assemble into distinct communities over space and time. Deciphering how microbiome dynamics are shaped by environmental variability is fundamental for understanding the structure and function of ecosystems. Here, we leveraged autonomous samplers and in situ sensors to investigate the taxonomic and functional seasonality of microbial communities in Arctic and Antarctic pelagic waters. Both datasets include amplicon sequences in approximately biweekly resolution; complemented by ~100 PacBio HiFi metagenomes covering all major seasonal shifts. In the West Spitsbergen Current (80°N), we demonstrate distinct succession of prokaryotic and microeukaryotic communities over four years; with recurrent, unimodal fluctuations in abundance. The succession of prokaryotic taxa and genes was organised into five modules, each harboring unique taxonomic and metabolic signatures − illustrating a finely tuned ecological landscape. For instance, Cand. Nitrosopumilus and the machinery to oxidise ammonia and reduce nitrite were unique to early polar night, while late summer was dominated by Amylibacter and sulfur compound metabolism; along with enrichment of Synechococcus and photosynthesis. Furthermore, seasonal modules varied in their degree of functional redundancy and in genetic diversity within the functions across years. In parallel, we study microbiome seasonality in the Weddell Sea (69°S). This “Last Ice Area” has yet encountered minimal impact of climate change; allowing to benchmark the ecological implications of future warming at unprecedented scale. This dataset includes monthly records of sinking particles collected via sediment traps; establishing a holistic picture of the biological carbon pump. Overall, polar day and night concurred with similar microbial contrasts as in the Arctic, attributed to both shared and unique Antarctic taxa; partly related to the markedly differing sea-ice and hydrographic dynamics. Overall, our evidence offers fundamental insights into the structuring of marine microbiomes under pronounced environmental variability; including the “bi-polarity” of temporal microbiome assembly.