This study evaluates the distribution and sources of thermogenic organic matter in the Baltic Sea water column, focusing on polycyclic aromatic hydrocarbons (PAH), dissolved black carbon (DBC), and the imprint of thermogenic organic matter on the dissolved organic matter (DOM) pool. The spatial patterns and complex interactions between land-based and atmospheric sources were assessed from Kiel Bay to Pomeranian Bight within the water column with the combined targeted and untargeted approaches. The findings emphasize the significant influence of terrestrial inputs from the Oder River and autochthonous production composing DOM. In the Pomeranian Bight, PAH and DBC concentrations strongly correlate with land-based discharge, while shipping emissions play a more prominent role in the Arkona Sea. The sea surface microlayer shows unique characteristics in DOM composition, with potential combustion products as an important source revealed by PAH and DOM analyses. Ultrahigh-resolution mass spectrometry identified combustion products, in the DOM pool, providing insights into anthropogenic impacts. This research contributes to a better understanding of the complex dynamics of thermogenic organic matter in coastal environments, highlighting the interplay between land-based sources, shipping emissions, and in-situ processes in the Baltic Sea region.