The fatty acid composition of two species of aquatic plants Myriophyllum spicatum, Elodea canadensis from the Angara River both under normal conditions and under the influence of hypothermia (30 °С) and cadmium chloride (100 mg/l) was studied by chromatography-mass-spectrometry. A comparative analysis of the fatty acid content and the values of the double bond index were carried out. Fatty acid composition of tissues studied species was species-specific and characterized by a relatively low content of saturated fatty acids. The main saturated acid in both species was palmitic acid (С16:0). Among the saturated fatty acids have been marked molecule with an odd number of carbon atoms - pentadecanoic (С15:0), heptadecanoic (С17:0) and heneicosanoic acid (С21:0). Heneico-sanoic acid was found only in the tissues Elodea canadensis. The most amount of unsaturated fatty acids were accounted for linoleic (С18:2П-6) and а-linolenic acid (С18:3П-3). The changes in the composition of fatty acids after 24 and 48 hours in response to the factors tested are shown. The differences in fatty acid composition changes in response to exposure to cadmium chloride and hyperthermia in the species studied have been found.