An outstanding challenge in viral ecology, in particular when working with aquatic viral metagenomes is the inability to link viral sequences to their hosts. Additionally, methods for processing viral metagenomes cause a loss of relevant ecological information namely, phenotypic information about the virion itself. In this study, we aimed to link viruses to their hosts, as well as to retain phenotypic information, through a combination of upstream and downstream processes. Pristine basement fluids were collected from CORK (circulation obviation retrofit kit) observatories, located on the flank of the Juan de Fuca Ridge (JdFR) and metagenomes from both the microbial (> 0.2 µm) and the viral (< 0.2 µm and > 100 kDa) size fractions were constructed. To retain phenotypic information about virions, and to reduce complexity, which facilitates viral genome reconstruction; intact viral particles were fractionated following separation on a CsCl gradient. Viral metagenomes were constructed from DNA extracted from each of 17 buoyant density fractions. Analysis of these 17 metaviromes indicated that physical fractionation resulted in enrichment of archaea virus-like sequences in low-density fractions. Assembly of viral metagenomes resulted in 34 closed (circularized) viral genomes, and 110 linear viral scaffolds. The discovery of CRISPRs has allowed connections to be made between viral metagenomes and microbial hosts because host-encoded CRISPR cassettes contain short virus-derived sequences. CRISPR elements were identified on 12,877 of the microbial raw reads indicating that viruses are likely to be actively infecting microbial populations in the JdFR flank basement fluids. The combination of recruitment of whole CRISPR elements to microbial genomic bins and the recruitment of CRISPR spacers to our viral metagenomes, allowed us to identify host groups infected by specific viral genomes. Additional analysis of taxonomically-identified microbial genomic bins revealed 50 prophages within microbial genomes. Through this study we have successfully linked deep subsurface viruses to microbial hosts.