Distributions of Δ14CTOC studied in bottom sediments collected during 2011–2016 in the Curonian Lagoon and in the open Baltic Sea indicated wide variations of Δ14CTOC values. Laboratory experiments on differential carbon utilization by Pseudomonas putida isolated from bottom sediments were carried out for better understanding of impacts of different sources on Δ14CTOC variations. Preferential glucose uptake (up to 80%) as a carbon source and a rather low (2–10%) inorganic carbon incorporation was found in media with diesel fuel. Pseudomonas putida a specific biomarker analyzed in biomass cultivated on the media with different carbon sources has been used to characterize microbial communities responsible for degradation of organic substances in bottom sediments. Large 14C depletions observed in sediments collected in the Gotland Deep of the Baltic Sea may indicate leakage from dumped chemical weapons.