The purpose of this study is to investigate historical and current mercury (Hg) contamination in the surface and core sediments of the Ambarli Port area. Textural parameters, total organic carbon (TOC), 210Pb and total Hg (THg) contents were measured. Mercury contamination of the sediments was assessed on the basis of the enrichment factor (EF), anthropogenic factor (AF), index of geoaccumulation (Igeo) and corresponding sediment quality guidelines. Most surface sediment samples were also non-toxic with mercury concentrations below the effects range-low (ERL) value, but mercury levels at five stations were between ERL and effects range-median (ERM) values, where occasional adverse effects concerning risk analysis are expected. The EF and Igeo analysis showed that there was no significant mercury enrichment and contamination in the core sediment before the 1650s, but values increased from then onwards to 2009 (being especially accelerated in line with port activities from 1989), disclosing a serious ecotoxicological risk to sediment-inhabited marine organisms.