Recently the importance of viruses has been investigated in an increasing number of aquatic habitats. However, the diversity and functionality of viruses within the deep biosphere as well as the impact they have on their microbial hosts remains largely unknown. Here, we have investigated the anoxic groundwater contained within three boreholes in the Äspö Hard Rock Laboratory, southeastern Sweden. The boreholes range in depth from 181 to 448 meter and contain newly infiltrated (<20 year) Baltic Sea water (modern marine), mixed water (undefined mixed), and ground water >1000 year old (old saline), respectively. Duplicate 0.2 μm filtered metagenomes from each borehole were individually assembled and, after sequences of likely cellular origin were removed, 3952 viral contigs containing >10 ORFs were further analyzed. Of all ORFs, 14% had similarity to known viruses, with 5% similar to Siphoviruse, 4% to Myoviruses, and 2% to Podoviruses. Further, more than 97% of the contigs shared <40% of their genes with previously isolated and sequenced phages, pointing towards the novelty of these viral communities. Only 2 contigs had high similarity to known viruses, sharing 72% of their ORFs with the temperate Vibrio phage VP882 and occurred in the old saline and undefined mixed waters. While 14% of the contigs occurred in all three aquifers, 70% of the contigs only occurred in the old saline and undefined mixed. The modern marine community was the most diverse with 30% unique contigs while the undefined mixed community had 8% unique contigs. Only one viral type was unique for the undefined mix: a contig similar to ssDNA inoviruses. All other contigs occurring in the undefined mixed also occurred in old saline. Overall, these data present unique information regarding the viral diversity, functionality, and spatial variations within the viral community in the deep biosphere.