Exchange of dissolved substances at the sediment–water interface provides an important link between the short-term and long-term geochemical cycles in the ocean. A second, as yet poorly understood sediment–water exchange is supported by low-temperature circulation of seawater through the oceanic basement underneath the sediments. From the basement, upwards diffusing oxygen and other dissolved species modify the sediment, whereas reaction products diffuse from the sediment down into the basement where they are transported by the basement fluid and released to the ocean. Here, we investigate the impact of this “second” route with respect to transport, release and consumption of oxygen, nitrate, manganese, nickel and cobalt on the basis of sediment cores retrieved from the Clarion Clipperton Zone (CCZ) in the equatorial Pacific Ocean. We show that in this abyssal ocean region characterised by low organic carbon burial and sedimentation rates vast areas exist where the downward- and upward-directed diffusive fluxes of oxygen meet so that the sediments are oxic throughout. This is especially the case where sediments are thin or in the proximity of faults. Oxygen diffusing upward from the basaltic crust into the sediment contributes to the degradation of sedimentary organic matter. Where the sediments are entirely oxic, nitrate produced in the upper sediment by nitrification is lost both by upward diffusion into the bottom water and by downward diffusion into the fluids circulating within the basement. Where the oxygen profiles do not meet, they are separated by a suboxic sediment interval characterised by Mn2+ in the porewater. Where porewater Mn2+ in the suboxic zones remains low, nitrate consumption is low and the sediment continues to deliver nitrate to the ocean bottom waters and basement fluid. We observe that at elevated porewater manganese concentrations, nitrate consumption exceeds production and nitrate diffuses from the basement fluid into the sediment. Within the suboxic zone, not only manganese but also cobalt and nickel are released into the porewater by reduction of Mn oxides, diffusing towards the oxic–suboxic fronts above and below where they precipitate, effectively removing these metals from the suboxic zone and concentrating them at the two oxic–suboxic redox boundaries. We show that not only do diffusive fluxes in the top part of deep-sea sediments modify the geochemical composition over time but also diffusive fluxes of dissolved constituents from the basement into the bottom layers of the sediment. Hence, the palaeoceanographic interpretation of sedimentary layers should carefully consider such deep secondary modifications in order to prevent the misinterpretation of primary signatures.