•Organic matter enriched in the sea surface microlayer at wind speed above 10 m s–1•Strong biotic and abiotic lipid reworking characterized the sea surface microlayer•Lipids contributed <10% to POC, indicative of a eutrophic system•Fluorescence analysis revealed a short river reach in the Gulf of Gdańsk We present the characterisation and distribution of organic matter (OM) within the sea surface microlayer (SML) and underlying water (ULW) collected in October 2015 at nine stations in the Baltic Sea, Gulf of Gdańsk, encompassing the Vistula River plume. The salinity of >7 throughout the transect indicated Vistula plume was possibly displaced westward by the preceding northerly and easterly winds between 5.7 and 10.7 ms–1 during the sampling campaign. Spectral analysis pointed to the highest contribution of aromatic and high molecular weight molecules (lowest spectral slope (SR) ratios and highest absorption coefficient at 254 nm (aCDOM(254)) at the first two stations near the river mouth, demonstrating a very limited influence of the river plume. Concentrations of surface-active organic substances (SAS) ranged from 0.28 to 0.60 mg L−1 in eq. Triton-X-100 in SML, and from 0.22 to 0.47 mg L−1 in eq. Triton-X-100 in the ULW, while POC concentrations ranged from 0.27 to 0.84 mg L−1 in SML and from 0.20 to 0.37 mg L−1 in ULW. Enrichment of SAS and POC detected at the highest wind speeds indicates rapid SML recovery by OM transported from the ULW. Low lipids to POC contribution, on average 5% and 7% in SML and ULW respectively, points to eutrophic conditions. Statistically significant negative correlation between SR and the Lipid:PIG ratio in SML and ULW suggests the production of lower molecular weight OM by phytoplankton living under favourable environmental conditions. Accumulation of lipid reserves triacylglycerols (TG) in the SML indicates more stressful plankton growth conditions compared to ULW.