Viruses that infect microbes are ecologically important on a global scale in terms of biogeochemical cycling of carbon, nutrients and energy in aquatic environments. Metagenomic studies, e.g. through Tara Oceans and the Pacific Ocean Virome, have improved our knowledge regarding the immense diversity of aquatic viruses and our understanding of spatial variations within the viral community. However, temporal dynamics of viral communities has been studied to a lesser extent. Between 2012 and 2015, 25 metagenomes, covering all seasons, were collected at the Linnaeus Microbial Observatory, in the Baltic Sea, a unique water body with a poorly investigated viral community. Illumina HiSeq sequencing provided 5.4-104.4 million pair end reads (2x101 bp and 2x126 bp) per metagenome sample. A co-assembly of all metagenomes resulted in 400,000 contigs >1 kbp. Through contig annotation, complete or nearly complete viral genomes could be identified. A large proportion of these contigs show little resemblance to previously sequenced viruses, nevertheless, contigs with similarities to known viruses were identified. These included contigs similar to the globally abundant T4 cyanophages and pelagiphages, known to infect Pelagibacter ubique, as well as less abundant Cellulophaga phages, isolated from the Baltic Sea. A large number of contigs were also similar to eukaryotic viruses, e.g. Phycodnaviridae known to infect algae of the phylum Chlorophyta. By recruiting the metagenome samples back to the co-assembly, temporal variations within the viral community, as represented by the contigs, could be distinguished. For example, reoccurring peaks in relative abundance of viruses infecting Synechococcus and Bathycoccus was observed during autumn. Overall, this study provides novel insights into the seasonal variability in diversity and functionality of marine viral communities and how viral populations potentially are linked with microbial successions.