An intertidal site in the Clyde Estuary, UK, was selected to evaluate the role of sediment geochemistry on the bioaccumulation of polychlorinated biphenyls (PCBs) by mussels (Mytilus edulis). The area had previously been identified as showing anomalously high levels of PCB contamination (over 1500 μg kg−1 total PCB in sediment, 22 congeners). Samples of surface sediment and M. edulis were collected from two closely located sites, one within the anomalous area and another representing typical PCB contamination in the estuary. Sediment samples were separated into grain size fractions and analysed for a range of biomarker compounds, PCBs and sediment mineralogy. The anomalous site showed an atypical association of PCBs with sediment properties, despite both locations showing influence of both petrogenic and pyrogenic organic contamination. Interrogation of data using correlation and principal component analysis showed that sediment mineralogy as well as organic matter composition influenced PCB congener distribution. One sediment source was found to control the PCB concentration in mussels at both locations and clay mineralogy appears to control PCB uptake by biota with preference for higher molecular weight congeners. Overall bioavailability is determined by sediment TOC.