Industries near ports rely on fossil fuels and are likely to release fossil carbon into nearby ecosystems. Release of hazardous compounds such as heavy metals and polycyclic aromatic hydrocarbons can be directly coupled with the fossil carbon use and those compounds can be accumulated in port sediments. However, fossil carbon fractions in sedimentary organic carbon (SOC) at ports have not been investigated. We analyzed both concentrations and radiocarbon isotope ratios of SOC in three types of ports: fishery, steelmaking, and multipurpose (where a ship terminal and a cement plant are included). Results demonstrated a clear distinction. The sediment at steelmaking port showed the highest fossil carbon proportion (up to 84%), while the sediment at fishery port consisted mostly of modern carbon. The sediment at multipurpose port had an intermediate, 36% of fossil carbon contribution. Our findings suggest that sediments near steel and other heavy industries are hotspots of fossil carbon, potentially harming benthic ecosystems.