In this study, the biogeochemical transformations of sulphur in organic-rich marine sediments in a Scottish fjord are investigated by a combination of pore water and sediment geochemistry with sulphide diffusive gradient thin-film probes and sulphate isotopic data (δ34S and δ18O). Particular attention is paid to sulphur cycling in the upper sediment profile where sulphate reduction occurs but free sulphide is below the detection limits of conventional pore water geochemical analysis but quantifiable by sulphide diffusive gradient thin film. In the uppermost part of the sediment core, δ18O sulphate decreased from near-sea water values to +7‰, indicating that anoxic sulphide oxidation dominated during this interval. Sulphate δ34S remained unchanged as there was no net sulphate reduction (i.e. reduction was balanced by re-oxidation). Below 4 cm depth, there was a slight increase in sulphate δ34S from 20‰ to 23‰ associated with minor accumulation of iron sulphide. The δ18O of the sulphate also increased, to around +10‰ at 10 cm depth, as a result of the isotopic exchange of sulphate–oxygen with pore water and/or sulphur disproportionation reactions mediated during sulphur cycling. These processes continued to increase the δ18O of the sulphate to 14‰ at 20 cm depth with no further change in the δ34S of the sulphate. Below 20 cm depth, free sulphide is detectable in pore waters and both the δ34S of the sulphate and sulphide increase with depth with an offset controlled by kinetic fractionation during bacterial sulphate reduction. The δ34S of the sedimentary organic fraction shifted towards lower, more bacteriogenic, values with depth in the profile, without any increase in the size of this sulphur pool. Thus, the organic sulphur fraction was open to interaction with bacteriogenic sulphide without the occurrence of net addition. Therefore, caution should be exercised when using sulphur isotopic compositions to infer simple net addition of bacteriogenic sulphide to the organic sulphur fraction.