Free fatty acids concentrations and composition in dissolved and particulate fraction of the Baltic Sea surface waters (The Gulf of Gda?sk, the Gda?sk Deep and the Gotland Deep) and the Vistula waters were determined by means of fatty acids coumaryl esters HPLC analysis. Total concentrations of dissolved fatty acids were stated between 0.14 and 13 mg ?dm-3, whereas of particulate fatty acids between 16 and 50 mg ? dm-3. The concentrations depended strongly on the time and location of sampling. Palmitic acid was the dominant one in all inves-tigated samples. It was revealed that the total concentration as well as the percentage composi-tion of individual acids (especially polyunsaturated acids) in surface waters were related to the intensity of biological processes of the investigated area. The autochthonous phytoplankton blooms were the main source of fatty acids in the Baltic Sea surface waters.