The Megalopolis Lignite Centre (MLC) is a lignite mining and power generation complex located in Southern Greece. In the present study, we investigate the influence of mining and combustion activities on the organic matter (OM) budget of the adjacent Alfeios River plain sediments. A total of 28 plain-sediment samples along with 13 lignite and ash samples from the MLC were collected. The sediment samples were collected from sites upstream and downstream, as well as from the vicinity of the MLC. Their OM and total organic carbon contents range from 0.9 to 43.4 and 0.2 to 24.0 wt %, respectively. The particulate OM was classified in coal-derived, carbonized particles and fresh tissues according to its origin. The different OM phases were quantified using maceral analysis on the sediments' light fraction obtained after heavy media separations. Approximately 75 vol % of the OM was of anthropogenic origin (coal and char particles) related to mining, transport, and combustion processes at the MLC, revealing a high contamination degree. The most contaminated sites were those in the vicinity of the MLC, but upstream and downstream sites also proved to contain high concentrations of anthropogenic OM. The polycyclic aromatic hydrocarbons content of the same sediments was very low, similar to pristine areas indicating that there is no contamination from such compounds in the area.