This article investigates variations of Δ14C and δ13C of total organic carbon (TOC) in sediments as well as in humic acids, lipid, and phospholipid fractions isolated from the surface (0–3 cm) sediment samples collected in the Curonian Lagoon and in the Baltic Sea. This study was performed to estimate relative contributions of the marine and terrestrial inputs to organic carbon in sediments, to assess a possible effect of petroleum hydrocarbon contamination on radiocarbon signatures, and to elucidate a possible leakage of chemical warfare agents (CWA) at the Gotland Deep dumpsite. Depleted Δ14C values of the TOC (down to −453‰) and of the total lipid extracts (down to −812.4‰) were detected at the CWA dumpsite. Application of the compound-specific method indicated a possible effect of CWA on depleted Δ14C and δ13C values in the investigated organic carbon fractions. The obtained results have indicated the different origin and behavior of lipids and TOC at the CWA dumpsite as compared to the area affected by the terrestrial-freshwater OC input. The Δ14C data of the TOC and total lipid extracts showed that recent sediments at the CWA dumpsite contain an excess of fossil carbon capable of influencing the 14C dating at the site.