These data were collected from surface sediments (0-5 cm) at sites located along the Athens Riviera and Salamina coastline, Greece. The sediments came from both oil-contaminated (via Agia Zoni II oil-spill) and uncontaminated sites and were first collected between September 2017 and April 2018. For sediments taken at each site, data includes hydrocarbon concentrations (alkanes and Polycyclic Aromatic Hydrocarbons (PAHs)), absolute microbial abundance (by Quantitative Polymerase Chain Reaction (qPCR)) of Bacteria, Archaea, and Fungi, and 16S rRNA amplicon libraries of Bacteria and Archaea. Additionally, nutrient concentrations (ammonia, nitrate, nitrite, silicate, and phosphate) were measured from seawater samples taken at the same sites. This study was conducted by the University of Essex, in partnerships with Archipelagos Institute of Marine Conservation and Cranfield University, and funded by the National Environmental Research Council and EnvEast DTP. Full details about this dataset can be found at https://doi.org/10.5285/acf464dc-be75-41b8-9688-f2ba4037ef53