Permian deep-water mudstones in the Tanqua Basin, South Africa, have been studied using geochemical and spectral gamma ray techniques. The mudstones occur as thick sequences between sand-rich submarine fans, but also occur as thinner mud-rich units within each fan. The interfan mudstones are interpreted to have accumulated during transgression and the consequent period of relatively high sea-level, while the submarine fans and their intrafan mudstones were deposited during regression and relatively low sea-level. Geochemical analyses revealed systematic differences between interfan and intrafan mudstones because the two types of mudstones have slightly different source lithologies. Differences between the two types of mudstone suggest that changes in relative sea-level played a role in controlling exposure of sediment source areas. There are geochemical signals that display systematic stratigraphic trends within both interfan and intrafan mudstones. These are best explained by gradual denudation, exposure and weathering of different lithologies within a single sediment source area. Both interfan and intrafan mudstones have uniform geochemical signals along the flow direction except for the relative amount of uranium. It is most likely that the basinward increase in uranium in the mudstones is the result of reduced clastic dilution of uranium-bearing pelagic fallout.