The environmental fate of hazardous hydrophobic pollutants in the marine environment is strongly influenced by organic carbon (OC) cycling. As an example, the seasonality in primary production impacts both water column OC quantity and quality, which may influence pollutant mass transport from the water column to the sediment. This study aims to better understand the role of water column OC variability for the fate of pollutants in a near-coastal area. We conducted an in situ sampling campaign in the coastal Baltic Proper during two seasons, summer and autumn. We used polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) as model compounds, as they represent a wide range in physicochemical properties and are ubiquitous in the environment. Freely dissolved, and OC-bound concentrations were studied in the water column and surface sediment. We found stronger sorption of pollutants to suspended particulate matter (SPM) during the summer compared to the autumn (average 0.6 and 0.9 log unit higher particle-water partition coefficients during summer for PAHs and PCBs). Our data suggest that stronger sorption mirrors a compositional change of the OC towards higher contribution of labile OC during the summer, characterized by two times higher fatty acid and 24% higher dicarboxylic acids in SPM during summer. High concentrations of OC in the water column during the autumn resulted in increased SPM-mediated sinking fluxes of pollutants. Our results suggest that future changes in primary production are prone to influence the bioavailability and mobility of pollutants in costal zones, potentially affecting the residence time of these hazardous substances in the circulating marine environment.