Earth's deep subsurface harbours a slow-growing but metabolically active microbial biosphere that plays important roles in nutrient cycling. The global biogeochemical cycles of carbon and sulfur, particularly, are influenced by redox reactions mediated by microorganisms in deep groundwater, sediments and rock. These subsurface biospheres extend across the continental-marine boundary and must be considered to understand the fluid chemistry of deep aquifers and potential reactions controlling naturally or anthropogenically sequestered C or S. Contemporary CO2 storage schemes in particular may require knowledge about subsurface microbial controls on C flow to avoid conversion of CO2 to CH4, or the transformation of co-contaminants like SO2 to sulfuric acid. This presentation explores the deep biosphere in both a terrestrial and a marine setting, where aqueous geochemistry and metagenomics were applied to unravel the distribution, phylogeny and activity of CO-oxidising and SO4-reducing bacteria. Key findings involve 1) dominance of a deep terrestrial aquifer by a single microorganism and the deactivation of anaerobic CO-oxidation pathways under CO2 stress, and 2) dominance of a deep marine aquifer at the crustal basement-sediment interface by one clade of aero-tolerant sulfate-reducing bacteria “fed” with SO4 circulating through seafloor basalt. These microbial consortia, in their respective settings, effectively control the form and fate of deeply circulating carbon and sulfur.