Viruses are estimated to comprise 1031 particles in the global biosphere making them the most abundant biotic entity on Earth, yet we are only beginning to grasp their diversity and ecological impacts. Bacteriophages (phages; viruses that infect bacteria and archaea) are ubiquitous in all environments. They exist as part of a complex microbial ecosystem and are central to microbial community structure. Enzymes encoded by their hosts, bacteria and archaea, catalyse all the major processes involved in global biogeochemical cycling, but knowledge of their co-occurring viruses is poor. Viruses play a crucial role in regulating host survival and productivity; they contribute to mortality, horizontal gene transfer, and the expression of viral auxiliary metabolic genes (AMGs). Understanding the relationship between viruses and their hosts is therefore key to understanding microbial physiology, population dynamics, and metabolic evolution. This project will shed light on viruses that are of significance to the ecosystem by linking them to microbial key players in the Baltic Sea. To do this, both the microbial and viral fraction of seawater has been collected off the coast of Öland, Sweden, between 2016−2020. Frequency of sampling has been approximately monthly for viral samples and biweekly for microbial samples, generating 204 metagenomic and viromic datasets. Using this long-term temporal dataset, we will explore the microbial and viral community in the Baltic Sea and address ecological and evolutionary drivers of microbial-viral interactions in a largely unexplored brackish ecosystem.