We studied lipids and fatty acids (FA) in bottom sediments from four Siberian water bodies, Bugach, Lesnoi and Krasnoyarsk freshwater reservoirs and brackish Shira lake, that differed in physico-chemical and biological conditions. We considered the potential of the bottom sediments as a feedstock for biodiesel production and estimated properties of the obtained biodiesel as a fuel on the basis of FA composition. Contents of lipids and FA in the sediments moderately varied and were generally close to the reported data from lacustrine and estuarine systems. We confirmed that long-term eutrophication of a water body resulted in the lipid-rich bottom sediments that make them a feedstock for biodiesel production. Each of the studied water bodies had specific FA composition of sediments likely due to different organic matter sources and transformation processes. Despite these differences in FA profiles, calculated key parameters (cetane number, iodine number and heat of combustion) of biodiesel produced from all the studied sediments met the limits established by current biodiesel standards. Thus, the variation in the sediment FA composition due to environmental characteristics of a water body likely has no principal significance for fuel properties of the obtained biodiesel.