Prokaryotes make up the majority of the biomass in sediment, which covers two thirds of the Earth’s surface. In sediment, prokaryotes and viruses play a role in cycling organic carbon and regulate the fluctuation of organic matter. In anoxic sediment, the relationships between geochemical gradients, genomic potential, and virus-host interactions remain understudied and poorly understood. We characterized the prokaryotic and viral diversity along the geochemical gradients of a laminated sediment core from an anoxic sinkhole, Blackwood Sinkhole, Bahamas. We analyzed the pore water chemistry (nutrients, carbon, nitrogen) and identified the various sources contributing to the preserved sedimentary organic matter (surrounding terrestrial inputs or authigenic primary productivity). We characterized the microbial community composition of specific stratigraphic layers using 16S ribosomal RNA gene sequencing and metagenomics to show that there is a microbial succession down the core. Finally, we looked at viral assemblages using metagenomics and viral production through virus-induced microbial experiments to characterize virus-host interactions and better understand the role of viral lysis in this system. Through the characterization of the relationships of microbes between each other and with their environment, we aimed to identify the role organic and inorganic matter availability plays in shaping viral and prokaryotic communities, as well as how microbial communities shape their environment.